Louis BECQUEY / biorseo

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Louis BECQUEY
0b17971f 2 parents ed92d4ff 78f08463

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...@@ -23,5 +23,11 @@ results/* ...@@ -23,5 +23,11 @@ results/*
23 log_of_the_run.sh 23 log_of_the_run.sh
24 logBadDesc.txt 24 logBadDesc.txt
25 gurobi.log 25 gurobi.log
26 -IL* 26 +temp/*
27 -HL* 27 +
28 +# data
29 +data/modules/BGSU/HL/3.2/diagnostic/*
30 +data/modules/BGSU/HL/3.2/lib/*
31 +data/modules/BGSU/IL/3.2/diagnostic/*
32 +data/modules/BGSU/IL/3.2/lib/*
33 +data/modules/DESC/*.desc
...\ No newline at end of file ...\ No newline at end of file
......
...@@ -2,8 +2,6 @@ ...@@ -2,8 +2,6 @@
2 CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128" 2 CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128"
3 IEIGEN="/usr/local/include/eigen3" 3 IEIGEN="/usr/local/include/eigen3"
4 INUPACK="/usr/local/include/nupack" 4 INUPACK="/usr/local/include/nupack"
5 -jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar" 5 +biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
6 -ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib" 6 +jar3dexec="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
7 -HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib" 7 +bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
8 -descfolder="/home/persalteas/Data/RNA/motifs/Rna3Dmotif/No_Redondance_DESC/"
9 -bypdir="/home/persalteas/Software/BayesPairing/bayespairing/src"
......
1 -This is a bi-objective integer programming algorithm. 1 +Biorseo (Bi-Objective RNA Structure Efficient Optimizer)
2 -It predicts the secondary structure of a RNA sequence with pieces of 3D information (non-canonical contacts) at some places, 2 +===================================
3 -by identifying zones that can fold like known motifs from the RNA 3D Motif Atlas. 3 +
4 +This tool predicts the secondary structure of a RNA sequence with pieces of 3D information (non-canonical contacts) at some places,
5 +by identifying zones that can fold like known modules from data like the RNA 3D Motif Atlas or Rna3Dmotifs.
6 +
7 +Contact : louis.becquey@univ-evry.fr
4 8
5 1/ How it works 9 1/ How it works
6 =================================== 10 ===================================
...@@ -8,24 +12,123 @@ INPUT: ...@@ -8,24 +12,123 @@ INPUT:
8 - An RNA sequence (tested with sequences ~100 bases) 12 - An RNA sequence (tested with sequences ~100 bases)
9 13
10 THEN 14 THEN
11 -- Identifies possible 2D folds with RNAsubopt. 15 +- **Pattern-matching step** : Find all possible occurrences of known RNAmodules in the query sequence, by finding subsequences of the querythat score well with the probabilistic models of the modules (like JAR3D, or BayesPairing)
12 -- Knowing possible 2D folds, locate every possibly unpaired loop (hairpin loop, internal loop, multiple loop...) 16 +- **Constraints definition step** : Define constraints on the secondary structure imposed by modules if they would be included (in this case, some of the canonical base-pairs are forbidden)
13 -- align each unpaired loop to the catalogue of models of known RNA motifs (The 3D Motif Atlas of the BGSU RNA group) 17 +- **Solve a bi-objective IP problem** : Find a secondary structure that satisfies as much as possible both the expected accuracy of the structure and a criterion taking into account module inclusions, by solving a bi-objective integer linear programming problem, using the previous constraints defined in the previous step.
14 -- retrieve a list of potential motif-insertion-sites in the RNA sequence. Use them to define the constraints for the IP problem.
15 -- Solve a bi-objective IP problem:
16 - * Maximize the expected accuracy of the secondary structure,
17 - * Maximize the number and size of motifs inserted in the structure.
18 18
19 OUTPUT: 19 OUTPUT:
20 -- A set of secondary structures from the pareto front, 20 +- A set of secondary structures from the Pareto front,
21 -- The list of known motif inserted in the corresponding structures (and the non-canonical contacts) 21 +- The list of known modules inserted inplace in the corresponding structures
22 -- (lower score structures from k-Pareto sets, not implemented yet.) 22 +
23 +2/ The different models
24 +==================================
25 +MODULE SOURCES
26 +
27 +Biorseo can be used with two modules datasets (yet):
28 +* Rna3Dmotifs (from the work of *Djelloul & Denise, 2008*), but with the 3D data of 2018
29 +* The RNA 3D Motif Atlas of BGSU's RNA lab (*Petrov et al, 2013*, see http://rna.bgsu.edu/rna3dhub/motifs/)
30 +* RNA-Bricks 2 or CaRNAval could theoretically be used, but are not supported (yet). You might write your own API.
23 31
24 -2/ Installation 32 +PATTERN MATCHING STEP
33 +- Use **simple pattern matching**. Rna3Dmotifs modules are available with sequence information. We use regular expressions to find those known loops in your query. This is the approach of RNA-MoIP (*Reinharz et al, 2012*), we deal the same way with short components and wildcards.
34 +
35 +- Use **JAR3D**. The RNA 3D Motif Atlas modules can be scored against a given loop sequence by an hybrid SCFG/MRF method (*Zirbel et al, 2015*). This first requires to identify potential loops, which is achieved by a run of RNAsubopt first.
36 +
37 +- Use **Bayesian networks with BayesPairing**. To accurately model probability dependancies between nucleotides, one can use BayesPairing to build bayesian networks of the modules (the RNA 3D Motif Atlas and Rna3Dmotifs are both supported). Then, sequences are sampled with the Bayesian network of a module, and we use regular expressions to find them in your query.
38 +
39 +OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
40 +
41 +* **Function A** : weights a module by its squared number of nucleotides (like RNA-MoIP).
42 +* **Function B** : weights a module by its number of components (strands) and penalizes it by the log^(_2) of its nucleotide size.
43 +* **Function C** : weights a module by its insertion site score (JAR3D or BayesPairing score).
44 +* **Function D** : weights a module by its number of components (strands) and insertion site score (JAR3D or BayesPairing score), and penalizes it by the log^(_2) of its nucleotide size.
45 +
46 +3/ Recommended uses
25 ================================== 47 ==================================
26 -- Download and install RNAsubopt from the ViennaRNA package (https://www.tbi.univie.ac.at/RNA/) 48 +- If **you know you have no pseudoknot**:
27 -- Download and install IBM ILOG Cplex optimization studio (https://www.ibm.com/analytics/cplex-optimizer), free academic account required 49 + * Benchmarks show Biorseo does not perform better than simpler tools like RNAsubopt alone. Please use RNAsubopt (ViennaRNA package) or Fold (RNAstructure package).
50 +
51 +- If you **might expect a pseudoknot, or don't know**:
52 + * The most promising method is the use of direct pattern matching with Rna3Dmotifs and function B. But this method is sometimes subject to combinatorial explosion issues. If you have a long RNA or a large number of loops, don't use it. Example:
53 + `./bin/biorseo -s PDB_00304.fa --descfolder ./data/modules/DESC --type B -o PDB_00304.rawB `
54 +
55 + * The use of the RNA 3D Motif Atlas placed by JAR3D and scored with function B is not subject to combinatorial issues, but performs a bit worse. It also returns less solutions. Example:
56 + `./bin/biorseo -s PDB_00304.fa --jar3dcsv PDB_00304.sites.csv --type B -o PDB_00304.jar3dB`
57 +
58 +
59 +4/ Installation
60 +==================================
61 +### DEPENDENCIES
62 +- Make sure you have Python 3.5+, Cmake, and a C++ compiler installed on your distribution.
63 +- Install automake and libboost-filesystem.
64 +- Download and install [IBM ILOG Cplex optimization studio](https://www.ibm.com/analytics/cplex-optimizer), an academic account is required. The free version is too limited, you must register as academic. This is also free.
65 +- Download and install Eigen: Get the latest Eigen archive from http://eigen.tuxfamily.org. Unpack it, and install it.
66 +```bash
67 +wget http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz -O eigen_src.tar.gz
68 +tar -xf eigen_src.tar.gz
69 +cd eigen-eigen-323c052e1731
70 +mkdir build
71 +cd build
72 +cmake ..
73 +sudo make install
74 +```
75 +- Download and install NUPACK: Register on [Nupack's website](http://www.nupack.org/downloads/source), download the source, unpack it, build it, and install it:
76 +```bash
77 +wget http://www.nupack.org/downloads/serve_file/nupack3.2.2.tar.gz
78 +tar -xf nupack3.2.2.tar.gz
79 +cd nupack3.2.2
80 +mkdir build
81 +cd build
82 +cmake ..
83 +make -j4
84 +sudo make install
85 +```
86 +
87 +### OPTIONAL DEPENDENCIES FOR USE OF JAR3D
88 +- Download and install RNAsubopt from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/).
28 - Download and install Java runtime (Tested with Java 10) 89 - Download and install Java runtime (Tested with Java 10)
29 -- Download and install the latest JAR3D executable "jar3d_releasedate.jar" and motif models in this folder (http://rna.bgsu.edu/data/jar3d/models/) 90 +- Download the latest JAR3D executable "*jar3d_releasedate.jar*", and latest IL and HL models from [here](http://rna.bgsu.edu/data/jar3d/models/).
30 - Note that for HL and ILs, only the latest version is required (not all the versions provided in the folders). 91 + Note that only the latest version is required (not all the versions provided in the folders).
31 -- Download and install a C++ compiler and building dependencies and utilities (g++ or clang, automake, libboost) 92 +
93 +### OPTIONAL DEPENDENCIES FOR USE OF BAYESPAIRING
94 +- Download and install RNAfold from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/).
95 +- Make sure you have Python 3.5+ with packages networkx, numpy, regex, wrapt and biopython
96 +- Clone the latest BayesPairing Git repo, and install it :
97 +```
98 +git clone http://jwgitlab.cs.mcgill.ca/sarrazin/rnabayespairing.git BayesPairing
99 +cd BayesPairing
100 +pip install .
101 +```
102 +
103 +### RNA3DMOTIFS DATA
104 +
105 +If you use Rna3Dmotifs, you need to get RNA-MoIP's .DESC dataset: download it from [GitHub](https://github.com/McGill-CSB/RNAMoIP/blob/master/CATALOGUE.tgz). Put all the .desc from the `Non_Redundant_DESC` folder into `./data/modules/DESC`. Otherwise, you also can run Rna3Dmotifs' `catalog` program to get your own DESC modules collection from updated 3D data (download [Rna3Dmotifs](https://rna3dmotif.lri.fr/Rna3Dmotif.tgz)). You also need to move the final DESC files into `./data/modules/DESC`.
106 +
107 +### THE RNA 3D MOTIF ATLAS DATA
108 +
109 +If not done during the installation of JAR3D, get the latest version of the HL and IL module models from the [BGSU website](http://rna.bgsu.edu/data/jar3d/models/) and extract the Zip files. Put the HL and IL folders into `./data/modules/BGSU`.
110 +
111 +### BUILDING
112 +* Clone this git repository : `git clone https://github.com/persalteas/biorseo.git` and `cd biorseo`.
113 +* Edit the file `EditMe` to set the paths of the above dependencies and data. Fileds that you will not use can be ignored (ex: bypdir if you do not use BayesPairing). Example of my setup:
114 + * CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio128_Student"
115 + * IEIGEN="/usr/local/include/eigen3"
116 + * INUPACK="/usr/local/include/nupack"
117 + * jar3dexec="/nhome/siniac/lbecquey/Software/jar3dbin/jar3d_2014-12-11.jar"
118 + * ILmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/IL/3.2/lib"
119 + * HLmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/HL/3.2/lib"
120 + * descfolder="/nhome/siniac/lbecquey/Data/RNA/motifs/Rna3Dmotifs/No_Redondance_DESC/"
121 + * bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
122 + * biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
123 +* You might want to edit `Makefile` if you are not using clang as compiler. For example, if you use g++, replace clang++ by g++.
124 +* Build it: `make -j4`
125 +* The working executable file is `./bin/biorseo`.
126 +
127 +### BAYESPAIRING USERS: PREPARE BAYESIAN NETWORKS
128 +We run an example job for it to build the bayesian networks of our modules.
129 +```
130 +cd rnabayespairing/src
131 +python3 parse_sequences.py -d rna3dmotif -seq ACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU -ss ".................................................................((...............)xxxx(...................................................)xxx).............."
132 +```
133 +Use `-d rna3dmotif` or `-d 3dmotifatlas` depending on the module source you are planning to use.
134 +This is a quite long step, but the bayesian networks will be ready for all the future uses.
......
1 ->E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
3 -(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
...\ No newline at end of file ...\ No newline at end of file
1 ->E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
1 -E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
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23 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 475.0000000 24.6241106
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34 -(((((((.(((((........[[[[....[[[[....{{{{.))))))))))))..........................]]]].....]]]]...........}}}}
1 -E.coli_alpha_operon_mRNA
2 -UGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGA
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192 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
193 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 6.5590302 27.7426287
194 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
195 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
196 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
197 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 6.5590302 27.7426287
198 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 + 3PYO.A.85 6.5590302 27.7426287
199 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
200 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
201 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 6.5590302 27.7426287
202 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 6.5590302 27.7426287
203 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 6.5590302 27.7426287
204 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 6.5590302 27.7426287
205 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
206 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1JZX.A.84 + 1YIT.0.13 + 2BTE.E.3 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
207 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
208 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
209 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 6.5590302 27.7426287
210 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2V49.A.72 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 6.5590302 27.7426287
211 -((.((((.((.((((.((...((((....))))...)).)).)).)))))).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1YIT.0.13 + 2BTE.E.3 + 2Z4N.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 6.5590302 27.7426287
212 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
213 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 7.5724746 24.6241106
214 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 7.5724746 24.6241106
215 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
216 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZE.A.89 + 3IZF.A.191 + 3PYO.A.85 7.5724746 24.6241106
217 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 7.5724746 24.6241106
218 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 7.5724746 24.6241106
219 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 7.5724746 24.6241106
220 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 7.5724746 24.6241106
221 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
222 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 7.5724746 24.6241106
223 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
224 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2V49.A.72 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZE.A.89 + 3IZF.A.191 + 3O58.1.74 7.5724746 24.6241106
225 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.196 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
226 -((.((.((..(((((.((...((........))...)).)).))).)).)).))(((...))).((.((.((..((.((.((.((...)).)))).)).)).)).)). + 1F1T.A.4 + 1FKA.A.92 + 1YIT.0.13 + 2BTE.E.3 + 2OM7.B.1 + 2VHN.B.71 + 3IZ9.A.80 + 3IZF.A.191 + 3O58.1.74 + 3O58.1.74 + 3PYO.A.85 7.5724746 24.6241106
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1 +#!/usr/bin/python3
2 +# coding=utf-8
3 +import sys
4 +import getopt
5 +from scipy import stats
6 +import subprocess
7 +from os import path, makedirs, getcwd, chdir, devnull
8 +import matplotlib.pyplot as plt
9 +from matplotlib import colors
10 +from math import sqrt
11 +from multiprocessing import Pool, cpu_count, Manager
12 +import multiprocessing
13 +import ast
14 +
15 +
16 +# ================== DEFINITION OF THE PATHS ==============================
17 +
18 +# Retrieve Paths from file EditMe
19 +jar3dexec = ""
20 +bypdir = ""
21 +biorseoDir = "."
22 +exec(compile(open(biorseoDir+"/EditMe").read(), '', 'exec'))
23 +runDir = path.dirname(path.realpath(__file__))
24 +outputDir = biorseoDir + "/results/"
25 +HLmotifDir = biorseoDir + "/data/modules/BGSU/HL/3.2/lib"
26 +ILmotifDir = biorseoDir + "/data/modules/BGSU/IL/3.2/lib"
27 +descfolder = biorseoDir + "/data/modules/DESC"
28 +
29 +
30 +# ================== CLASSES AND FUNCTIONS ================================
31 +
32 +
33 +class NoDaemonProcess(multiprocessing.Process):
34 + @property
35 + def daemon(self):
36 + return False
37 +
38 + @daemon.setter
39 + def daemon(self, value):
40 + pass
41 +
42 +
43 +class NoDaemonContext(type(multiprocessing.get_context())):
44 + Process = NoDaemonProcess
45 +
46 +# We sub-class multiprocessing.pool.Pool instead of multiprocessing.Pool
47 +# because the latter is only a wrapper function, not a proper class.
48 +
49 +
50 +class MyPool(multiprocessing.pool.Pool):
51 + def __init__(self, *args, **kwargs):
52 + kwargs['context'] = NoDaemonContext()
53 + super(MyPool, self).__init__(*args, **kwargs)
54 +
55 +
56 +class Loop:
57 + def __init__(self, header, subsequence, looptype, position):
58 + self.header = header
59 + self.seq = subsequence
60 + self.type = looptype
61 + self.position = position
62 +
63 + def get_header(self):
64 + return self.header
65 +
66 + def subsequence(self):
67 + return self.seq
68 +
69 +
70 +class InsertionSite:
71 + def __init__(self, loop, csv_line):
72 + # BEWARE : jar3d csv output is crap because of java's locale settings.
73 + # On french OSes, it uses commas to delimit the fields AND as floating point delimiters !!
74 + # Parse with caution, and check what the csv output files look like on your system...
75 + info = csv_line.split(',')
76 + self.loop = loop # the Loop object that has been searched with jar3d
77 + # position of the loop's components, so the motif's ones, in the query sequence.
78 + self.position = loop.position
79 + # Motif model identifier of the RNA 3D Motif Atlas
80 + self.atlas_id = info[2]
81 + # alignment score of the subsequence to the motif model
82 + self.score = int(float(info[4]))
83 + # should the motif model be inverted to fit the sequence ?
84 + self.rotation = int(info[-2])
85 +
86 + def __lt__(self, other):
87 + return self.score < other.score
88 +
89 + def __gt__(self, other):
90 + return self.score > other.score
91 +
92 +
93 +class Job:
94 + def __init__(self, command=[], function=None, args=[], how_many_in_parallel=0, priority=1, timeout=None, checkFunc=None, checkArgs=[]):
95 + self.cmd_ = command
96 + self.func_ = function
97 + self.args_ = args
98 + self.checkFunc_ = checkFunc
99 + self.checkArgs_ = checkArgs
100 + self.priority_ = priority
101 + self.timeout_ = timeout
102 + if not how_many_in_parallel:
103 + self.nthreads = cpu_count()
104 + elif how_many_in_parallel == -1:
105 + self.nthreads = cpu_count() - 1
106 + else:
107 + self.nthreads = how_many_in_parallel
108 +
109 +
110 +class BiorseoInstance:
111 + def __init__(self, argv):
112 + # set default options
113 + self.type = "dpm"
114 + self.modules = "desc"
115 + self.func = 'B'
116 + self.outputf = outputDir
117 + self.jobcount = 0
118 +
119 + # Parse options
120 + try:
121 + opts, args = getopt.getopt(
122 + argv, "hil::o:", ["type=", "func=", "modules="])
123 + except getopt.GetoptError:
124 + print("Please provide arguments !")
125 + sys.exit(2)
126 + for opt, arg in opts:
127 + if opt == "-h":
128 + print("biorseo.py -i myRNA.fa -o myRNA.jar3dB --type jar3d --func B")
129 + sys.exit()
130 + elif opt == "-i":
131 + self.inputfile = arg
132 + self.mode = 0 # single sequence mode
133 + elif opt == "-l":
134 + self.inputfile = arg
135 + self.mode = 1 # batch mode
136 + elif opt == "-o":
137 + self.outputf = arg # output file or folder...
138 + elif opt == "--func":
139 + if arg in ['A', 'B', 'C', 'D']:
140 + self.func = arg
141 + else:
142 + raise "Unknown scoring function " + arg
143 + elif opt == "--type":
144 + if arg in ['dpm', 'jar3d', 'byp']:
145 + self.type = arg
146 + else:
147 + raise "Unknown pattern matching method " + arg
148 + elif opt == "--modules":
149 + if arg in ['desc', 'bgsu']:
150 + self.modules = arg
151 + else:
152 + raise "Unsupported module model type " + arg
153 + else:
154 + raise "Unknown option " + opt
155 +
156 + if self.mode:
157 + # Create a job manager
158 + self.manager = Manager()
159 + self.running_stats = self.manager.list()
160 + self.running_stats.append(0) # n_launched
161 + self.running_stats.append(0) # n_finished
162 + self.running_stats.append(0) # n_skipped
163 + self.fails = self.manager.list()
164 +
165 + # Create the output folder
166 + subprocess.call(["mkdir", "-p", self.outputf])
167 +
168 + def enumerate_loops(self, s):
169 + def resort(unclosedLoops):
170 + loops.insert(len(loops)-1-unclosedLoops, loops[-1])
171 + loops.pop(-1)
172 +
173 + opened = []
174 + openingStart = []
175 + closingStart = []
176 + loops = []
177 + loopsUnclosed = 0
178 + consecutiveOpenings = []
179 + if s[0] == '(':
180 + consecutiveOpenings.append(1)
181 + consecutiveClosings = 0
182 +
183 + lastclosed = -1
184 + previous = ''
185 + for i in range(len(s)):
186 +
187 + # If we arrive on an unpaired segment
188 + if s[i] == '.':
189 + if previous == '(':
190 + openingStart.append(i-1)
191 + if previous == ')':
192 + closingStart.append(i-1)
193 +
194 + # Opening basepair
195 + if s[i] == '(':
196 + if previous == '(':
197 + consecutiveOpenings[-1] += 1
198 + else:
199 + consecutiveOpenings.append(1)
200 + if previous == ')':
201 + closingStart.append(i-1)
202 +
203 + # We have something like (...(
204 + if len(openingStart) and openingStart[-1] == opened[-1]:
205 + # Create a new loop starting with this component.
206 + loops.append([(openingStart[-1], i)])
207 + openingStart.pop(-1)
208 + loopsUnclosed += 1
209 + # We have something like )...( or even )(
210 + if len(closingStart) and closingStart[-1] == lastclosed:
211 + # Append a component to existing multiloop
212 + loops[-1].append((closingStart[-1], i))
213 + closingStart.pop(-1)
214 +
215 + opened.append(i)
216 +
217 + # Closing basepair
218 + if s[i] == ')':
219 + if previous == ')':
220 + consecutiveClosings += 1
221 + else:
222 + consecutiveClosings = 1
223 + # This is not supposed to happen in real data, but whatever.
224 + if previous == '(':
225 + openingStart.append(i-1)
226 +
227 + # We have something like (...) or ()
228 + if len(openingStart) and openingStart[-1] == opened[-1]:
229 + # Create a new loop, and save it as already closed (HL)
230 + loops.append([(openingStart[-1], i)])
231 + openingStart.pop(-1)
232 + resort(loopsUnclosed)
233 + # We have something like )...)
234 + if len(closingStart) and closingStart[-1] == lastclosed:
235 + # Append a component to existing multiloop and close it.
236 + loops[-1].append((closingStart[-1], i))
237 + closingStart.pop(-1)
238 + loopsUnclosed -= 1
239 + resort(loopsUnclosed)
240 +
241 + if i+1 < len(s):
242 + if s[i+1] != ')': # We are on something like: ).
243 + # an openingStart has not been correctly detected, like in ...((((((...)))...)))
244 + if consecutiveClosings < consecutiveOpenings[-1]:
245 + # Create a new loop (uncompleted)
246 + loops.append([(opened[-2], opened[-1])])
247 + loopsUnclosed += 1
248 +
249 + # We just completed an HL+stem, like ...(((...))).., we can forget its info
250 + if consecutiveClosings == consecutiveOpenings[-1]:
251 + consecutiveClosings = 0
252 + consecutiveOpenings.pop(-1)
253 + else: # There are still several basepairs to remember, forget only the processed ones, keep the others
254 + consecutiveOpenings[-1] -= consecutiveClosings
255 + consecutiveClosings = 0
256 +
257 + else: # We are on something like: ))
258 + # we are on an closingStart that cannot be correctly detected, like in ...(((...(((...))))))
259 + if consecutiveClosings == consecutiveOpenings[-1]:
260 + # Append a component to the uncomplete loop and close it.
261 + loops[-1].append((i, i+1))
262 + loopsUnclosed -= 1
263 + resort(loopsUnclosed)
264 + # Forget the info about the processed stem.
265 + consecutiveClosings = 0
266 + consecutiveOpenings.pop(-1)
267 +
268 + opened.pop(-1)
269 + lastclosed = i
270 +
271 + previous = s[i]
272 + # print(i,"=",s[i],"\t", "consec. Op=", consecutiveOpenings,"Cl=",consecutiveClosings)
273 +
274 + return(loops)
275 +
276 + def launch_JAR3D_worker(self, loop):
277 + # write motif to a file
278 + newpath = getcwd()+'/'+loop.header[1:]
279 + if not path.exists(newpath):
280 + makedirs(newpath)
281 + chdir(newpath)
282 + filename = loop.header[1:]+".fasta"
283 + fasta = open(filename, 'w')
284 + fasta.write('>'+loop.get_header()+'\n'+loop.subsequence()+'\n')
285 + fasta.close()
286 +
287 + # Launch Jar3D on it
288 + if loop.type == 'h':
289 + cmd = ["java", "-jar", jar3dexec, filename, HLmotifDir+"/all.txt",
290 + loop.header[1:]+".HLloop.csv", loop.header[1:]+".HLseq.csv"]
291 + else:
292 + cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt",
293 + loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"]
294 + nowhere = open(devnull, 'w')
295 + logfile = open("log_of_the_run.sh", 'a')
296 + logfile.write(' '.join(cmd))
297 + logfile.write("\n")
298 + logfile.close()
299 + subprocess.call(cmd, stdout=nowhere)
300 + nowhere.close()
301 +
302 + # Retrieve results
303 + insertion_sites = []
304 + if loop.type == 'h':
305 + capstype = "HL"
306 + else:
307 + capstype = "IL"
308 + csv = open(loop.header[1:]+".%sseq.csv" % capstype, 'r')
309 + l = csv.readline()
310 + while l:
311 + if "true" in l:
312 + insertion_sites.append(InsertionSite(loop, l))
313 + l = csv.readline()
314 + csv.close()
315 +
316 + # Cleaning
317 + chdir("..")
318 + subprocess.call(["rm", "-r", loop.header[1:]])
319 + return insertion_sites
320 +
321 + def launch_JAR3D(self, seq_, basename):
322 + rnasubopt_preds = []
323 + # Extracting probable loops from RNA-subopt structures
324 + rna = open(outputDir + basename + ".subopt", "r")
325 + lines = rna.readlines()
326 + rna.close()
327 + for i in range(2, len(lines)):
328 + ss = lines[i].split(' ')[0]
329 + if ss not in rnasubopt_preds:
330 + rnasubopt_preds.append(ss)
331 + HLs = []
332 + ILs = []
333 + for ss in rnasubopt_preds:
334 + loop_candidates = self.enumerate_loops(ss)
335 + for loop_candidate in loop_candidates:
336 + if len(loop_candidate) == 1 and loop_candidate not in HLs:
337 + HLs.append(loop_candidate)
338 + if len(loop_candidate) == 2 and loop_candidate not in ILs:
339 + ILs.append(loop_candidate)
340 + # Retrieve subsequences corresponding to the possible loops
341 + loops = []
342 + for i, l in enumerate(HLs):
343 + loops.append(
344 + Loop(">HL%d" % (i+1), seq_[l[0][0]-1:l[0][1]], "h", l))
345 + for i, l in enumerate(ILs):
346 + loops.append(
347 + Loop(">IL%d" % (i+1), seq_[l[0][0]-1:l[0][1]]+'*'+seq_[l[1][0]-1:l[1][1]], "i", l))
348 + # Scanning loop subsequences against motif database
349 + pool = MyPool(processes=cpu_count())
350 + insertion_sites = [x for y in pool.map(
351 + self.launch_JAR3D_worker, loops) for x in y]
352 + insertion_sites.sort(reverse=True)
353 + # Writing results to CSV file
354 + c = 0
355 + resultsfile = open(outputDir+basename+".sites.csv", "w")
356 + resultsfile.write("Motif,Rotation,Score,Start1,End1,Start2,End2\n")
357 + for site in insertion_sites:
358 + if site.score > 10:
359 + c += 1
360 + string = "FOUND with score %d:\t\t possible insertion of motif " % site.score + site.atlas_id
361 + if site.rotation:
362 + string += " (reversed)"
363 + string += (" on " + site.loop.get_header() + " at positions")
364 + resultsfile.write(site.atlas_id+',' +
365 + str(bool(site.rotation))+",%d" % site.score+',')
366 + positions = [','.join([str(y) for y in x]) for x in site.position]
367 + if len(positions) == 1:
368 + positions.append("-,-")
369 + resultsfile.write(','.join(positions)+'\n')
370 + resultsfile.close()
371 +
372 + def launch_BayesPairing(self, module_type, seq_, header_, basename):
373 + chdir(bypdir)
374 +
375 + cmd = ["python3", "parse_sequences.py", "-seq", outputDir +
376 + basename + ".fa", "-d", module_type, "-interm", "1"]
377 +
378 + logfile = open("log_of_the_run.sh", 'a')
379 + logfile.write(" ".join(cmd))
380 + logfile.write("\n")
381 + logfile.close()
382 +
383 + out = subprocess.check_output(cmd).decode('utf-8')
384 + BypLog = out.split('\n')
385 + idx = 0
386 + l = BypLog[idx]
387 + while l[:3] != "PUR":
388 + idx += 1
389 + l = BypLog[idx]
390 + insertion_sites = [x for x in ast.literal_eval(l.split(":")[1][1:])]
391 + if module_type == "rna3dmotif":
392 + rna = open(outputDir + basename + ".byp.csv", "w")
393 + else:
394 + rna = open(outputDir + basename + ".bgsubyp.csv", "w")
395 + rna.write("Motif,Score,Start1,End1,Start2,End2...\n")
396 + for i, module in enumerate(insertion_sites):
397 + if len(module):
398 + for (score, positions, sequence) in zip(*[iter(module)]*3):
399 + pos = []
400 + q = -2
401 + for p in positions:
402 + if p-q > 1:
403 + pos.append(q)
404 + pos.append(p)
405 + q = p
406 + pos.append(q)
407 + rna.write(module_type+str(i)+','+str(int(score)))
408 + for (p, q) in zip(*[iter(pos[1:])]*2):
409 + if q > p:
410 + rna.write(','+str(p)+','+str(q))
411 + rna.write('\n')
412 + rna.close()
413 +
414 + def execute_job(self, j):
415 + if j.checkFunc_ is not None:
416 + if j.checkFunc_(*j.checkArgs_):
417 + self.running_stats[2] += 1
418 + print("["+str(self.running_stats[0]+self.running_stats[2]) +
419 + '/'+str(self.jobcount)+"]\tSkipping a finished job")
420 + return 0
421 + self.running_stats[0] += 1
422 + if len(j.cmd_):
423 + logfile = open("log_of_the_run.sh", 'a')
424 + logfile.write(" ".join(j.cmd_))
425 + logfile.write("\n")
426 + logfile.close()
427 + print("["+str(self.running_stats[0]+self.running_stats[2]) +
428 + '/'+str(self.jobcount)+"]\t"+" ".join(j.cmd_))
429 + r = subprocess.call(j.cmd_, timeout=j.timeout_)
430 + elif j.func_ is not None:
431 + print("["+str(self.running_stats[0]+self.running_stats[2])+'/'+str(self.jobcount) +
432 + "]\t"+j.func_.__name__+'('+", ".join([a for a in j.args_])+')')
433 + try:
434 + r = j.func_(*j.args_)
435 + except:
436 + r = 1
437 + pass
438 + if r:
439 + self.fails.append(j)
440 + self.running_stats[1] += 1
441 + return r
442 +
443 + def check_result_existence(self, datatype, method, function, with_PK, basename):
444 + folder = self.outputf+"PK/" if with_PK else self.outputf+"noPK/"
445 + if datatype == "bgsu":
446 + if method == "jar3d":
447 + extension = ".jar3d"
448 + elif method == "byp":
449 + extension = ".bgsubyp"
450 + else:
451 + raise "Unknown method !"
452 + elif datatype == "desc":
453 + if method == "dpm":
454 + extension = ".raw"
455 + elif method == "byp":
456 + extension = ".byp"
457 + else:
458 + raise "Unknown method !"
459 + else:
460 + raise "Unknown data type !"
461 + return path.isfile(folder + basename + extension + function)
462 +
463 + def check_csv_existence(self, datatype, method, basename):
464 + if datatype == "bgsu":
465 + if method == "jar3d":
466 + extension = ".sites.csv"
467 + elif method == "byp":
468 + extension = ".bgsubyp.csv"
469 + else:
470 + raise "Unknown method !"
471 + elif datatype == "desc":
472 + if method == "byp":
473 + extension = ".byp.csv"
474 + else:
475 + raise "You cannot use " + method + " with " + datatype + " data !"
476 + else:
477 + raise "Unknown data type !"
478 + return path.isfile(self.outputf + basename + extension)
479 +
480 +
481 +if __name__ == "__main__":
482 + BiorseoInstance(sys.argv)
...@@ -8,7 +8,7 @@ ...@@ -8,7 +8,7 @@
8 #include <string> 8 #include <string>
9 #include <vector> 9 #include <vector>
10 10
11 -using Eigen::MatrixXf, Eigen::Matrix; 11 +using Eigen::MatrixXf;
12 using std::map; 12 using std::map;
13 using std::pair; 13 using std::pair;
14 using std::string; 14 using std::string;
......
1 +>>__'BRANCHPOINT_HELIX_FROM_YEAST_AND_BINDING_SITE_FOR_PHAGE_GA/MS2_COAT_PROTEINS,_NMR,_12_STRUCTURES_'_(PDB_00002)
2 +GGCGUAAGGAUUACCUAUGCC
3 +(((((.(((....))))))))
4 +>>__'LOOP_D/LOOP_E_ARM_OF_E._COLI_5S_RRNA,_NMR,_9_STRUCTURES_'_(PDB_00004)
5 +GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
6 +(((((((((((((((((((...)))))))))))))))))))
7 +>>__'NMR_STRUCTURE_OF_A_CLASSICAL_PSEUDOKNOT:_INTERPLAY_OF_SINGLE-AND_DOUBLE-STRANDED_RNA,_24_STRUCTURES_'_(PDB_00005)
8 +GGGAGCUCAACUCUCCCCCCCUUUUCCGAGGGUCAUCGGAACCA
9 +(((((.......)))))[[[...((((((]]]...))))))...
10 +>>__'SOLUTION_STRUCTURE_OF_A_SUBSTRATE_FOR_THE_ARCHAEAL_PRE-TRNA_SPLICING_ENDONUCLEASES:_THE_BULGE-HELIX-BULGE_MOTIF,_NMR,_12_STRUCTURES_'_(PDB_00006)
11 +GGGUGACUCCAGAGGUCGAGAGACCGGAGAUAUCACCC
12 +((((((((((...((((....))))))))...))))))
13 +>>__'UGAA_EUKARYOTIC_RIBOSOMAL_RNA_TETRALOOP,_NMR,_13_STRUCTURES_'_(PDB_00007)
14 +GGUGUGAACACC
15 +((((....))))
16 +>>__'HIV-2_TAR-ARGININAMIDE_COMPLEX,_NMR,_20_STRUCTURES_'_(PDB_00010)
17 +GGCCAGAUUGAGCCUGGGAGCUCUCUGGCC
18 +(((((((..((((......)))))))))))
19 +>>__'CIS-ACTING_RNA_REGULATORY_ELEMENT_(HIV-1_TAR),_NMR,_20_STRUCTURES_'_(PDB_00012)
20 +GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
21 +..(((....((((......)))).)))..
22 +>>__'IRON_RESPONSIVE_ELEMENT_RNA_HAIRPIN,_NMR,_15_STRUCTURES_'_(PDB_00013)
23 +GGAGUGCUUCAACAGUGCUUGGACGCUCC
24 +((((((.((.((......)).))))))))
25 +>>__'THE_STRUCTURE_OF_THE_ISOLATED,_CENTRAL_HAIRPIN_OF_THE_HDV_ANTIGENOMIC_RIBOZYME,_NMR,_10_STRUCTURES_'_(PDB_00014)
26 +GGCACCUCCUCGCGGUGCC
27 +(((((((.....)))))))
28 +>>__'HAIRPIN_WITH_AGAU_TETRALOOP,_NMR,_3_STRUCTURES_'_(PDB_00016)
29 +GCUCCAGAUGGAGCG
30 +(((((....))))).
31 +>>__'NMR_STRUCTURE_OF_THE_DIMER_INITIATION_COMPLEX_OF_HIV-1_GENOMIC_RNA,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00018)
32 +GGCAAUGAAGCGCGCACGUUGCCGGCAAUGAAGCGCGCACGUUGCC
33 +(((((((.[[..[[[[)))))))(((((((.]]]]..]])))))))
34 +>>__'S8_RRNA_BINDING_SITE_FROM_E._COLI,_NMR,_6_STRUCTURES_'_(PDB_00019)
35 +GGGAUACUGCUUCGGUAAGUCCC
36 +((((..((((....)).))))))
37 +>>__'RNA_LOOP-LOOP_COMPLEX:_THE_COLE1_INVERTED_LOOP_SEQUENCE,_NMR,_8_STRUCTURES_'_(PDB_00020)
38 +GGCAACGGAUGGUUCGUUGCCGCACCGAACCAUCCGGUGC
39 +((((((([[[[[[[)))))))((((((]]]]]]]))))))
40 +>>__'SL3_HAIRPIN_FROM_THE_PACKAGING_SIGNAL_OF_HIV-1,_NMR,_11_STRUCTURES_'_(PDB_00021)
41 +GGACUAGCGGAGGCUAGUCC
42 +((((((((....))))))))
43 +>>__'HIV-1_RNA_A-RICH_HAIRPIN_LOOP_'_(PDB_00022)
44 +GGCGACGGUGUAAAAAUCUCGCC
45 +(((((.((((....)))))))))
46 +>>__'STABILIZATION_OF_THE_ANTICODON_STEM-LOOP_OF_TRNALYS,3_BY_AN_A+C_BASE_PAIR_AND_BY_PSEUDOURIDINE,_NMR,_1_STRUCTURE_'_(PDB_00024)
47 +UCAGACUUUUAAUCUGA
48 +((((((.....))))))
49 +>>__'STABILIZATION_OF_THE_ANTICODON_STEM-LOOP_OF_TRNALYS,3_BY_AN_A+C_BASE_PAIR_AND_BY_PSEUDOURIDINE,_NMR,_1_STRUCTURE_'_(PDB_00025)
50 +UCAGACUUUUAAUCUGA
51 +(((((((...)))))))
52 +>>__'STRUCTURE_OF_THE_RIBOZYME_SUBSTRATE_HAIRPIN_OF_NEUROSPORA_VS_RNA._A_CLOSE_LOOK_AT_THE_CLEAVAGE_SITE_'_(PDB_00040)
53 +GUGCGAAGACGAAAGUCCGAGCGC
54 +((((((((((....))))))))))
55 +>>__'SOLUTION_STRUCTURE_OF_THE_PSEUDOKNOT_OF_SRV-1_RNA,_INVOLVED_IN_RIBOSOMAL_FRAMESHIFTING_'_(PDB_00041)
56 +GCGGCCAGCUCCAGGCCGCCAAACAAUAUGGAGCAC
57 +((((((.[[[[[[)))))).........]]]]]]..
58 +>>__'NMR_ANALYSIS_OF_HELIX_I_FROM_THE_5S_RNA_OF_ESCHERICHIA_COLI_'_(PDB_00048)
59 +UUGCCUGGCGGCAACUGCCAGGCAU
60 +..(((((((((...)))))))))..
61 +>>__'NMR_STRUCTURE_OF_STEM_LOOP_SL2_OF_THE_HIV-1_PSI_RNA_PACKAGING_SIGNAL_REVEALS_A_NOVEL_A-U-A_BASE-TRIPLE_PLATFORM_'_(PDB_00051)
62 +GGCGACUGGUGAGUACGCC
63 +(((((((....)).)))))
64 +>>__'CRYSTAL_STRUCTURE_OF_A_BIOTIN-BINDING_RNA_PSEUDOKNOT_'_(PDB_00053)
65 +ACCGUCAGAGGACACGGUUAAAAAGUCCUC
66 +[[[[[..((((((]]]]]......))))))
67 +>>__'SOLUTION_STRUCTURE_OF_THE_KISSING_DIMER_OF_H3_GACG_STEM-_LOOP_IN_THE_5\'-END_DIMERIZATION_SIGNAL_OF_MOLONEY_MURINE_LEUKEMIA_VIRUS_GENOMIC_RNA_'_(PDB_00056)
68 +GGUGGGAGACGUCCCACCGGUGGGAGACGUCCCACC
69 +(((((((..[[)))))))(((((((..]])))))))
70 +>>__'SOLUTION_STRUCTURE_OF_THE_RNASE_P_RNA_(M1_RNA)_P4_STEM_OLIGORIBONUCLEOTIDE_'_(PDB_00057)
71 +GGAAGUCCGGUCUUCGGACCGGCUUCC
72 +(((((.(((((......))))))))))
73 +>>__'SOLUTION_STRUCTURE_OF_RNASE_P_RNA_(M1_RNA)_P4_STEM_OLIGORIBONUCLEOTIDE_COMPLEXED_WITH_COBALT_(III)_HEXAMINE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00059)
74 +GGAAGUCCGGUCUUCGGACCGGCUUCC
75 +(((((.(((((......))))))))))
76 +>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_RNA_DOMAIN_IIID_'_(PDB_00065)
77 +GGCCGAGUAGUGUUGGGUCGCGAAAGGCC
78 +.(((((.(((((......)))))))))).
79 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_TRNA(LYS3)_WITH_T6A_MODIFICATION_AT_POSITION_37_'_(PDB_00068)
80 +GCAGACUUUUAAUCUGC
81 +((((((.....))))))
82 +>>__'NMR_STRUCTURE_OF_THE_690_LOOP_OF_16_S_RRNA_OF_E._COLI_'_(PDB_00069)
83 +GGCGGUGAAAUGCC
84 +(((((....)))))
85 +>>__'NMR_VALIDATED_MODEL_OF_DOMAIN_IIID_OF_HEPATITIS_C_VIRUS_INTERNAL_RIBOSOME_ENTRY_SITE_'_(PDB_00073)
86 +GCCGAGUAGUGUUGGGUCGCGAAAGGC
87 +(((((.(((((......))))))))))
88 +>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAACU_AS_PART_OF_HAIRPIN_R(GCGUUAACUCGCA)_'_(PDB_00083)
89 +GCGUUAACUCGCA
90 +((((....)))).
91 +>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAGU_AS_PART_OF_HAIRPIN_R(GCGUUAAGUCGCA)_'_(PDB_00084)
92 +GCGUUAAGUCGCA
93 +((((....)))).
94 +>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAUU_AS_PART_OF_HAIRPIN_R(GCGUUAAUUCGCA)_'_(PDB_00085)
95 +GCGUUAAUUCGCA
96 +((((....)))).
97 +>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAAU_AS_PART_OF_HAIRPIN_R(GCGUUAAAUCGCA)_'_(PDB_00086)
98 +GCGUUAAAUCGCA
99 +((((....)))).
100 +>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UCAAUU_AS_PART_OF_HAIRPIN_R(GCGUCAAUUCGCA)_'_(PDB_00087)
101 +GCGUCAAUUCGCA
102 +((((....)))).
103 +>>__'SOLUTION_STRUCTURE_OF_THE_VS_RIBOZYME_SUBSTRATE_STEM-LOOP_'_(PDB_00088)
104 +GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC
105 +((((((((((((......))))))))))))
106 +>>__'SOLUTION_STRUCTURE_OF_THE_A_LOOP_OF_23S_RIBOSOMAL_RNA_'_(PDB_00089)
107 +GGCUGGCUGUUCGCCAGCC
108 +((((((((...))))))))
109 +>>__'SOLUTION_STRUCTURE_OF_THE_A_LOOP_OF_23S_RIBOSOMAL_RNA._'_(PDB_00090)
110 +GGCUGGCUGUUCGCCAGCC
111 +((((((((...))))))))
112 +>>__'THE_SOLUTION_STRUCTURE_OF_THE_MUTANT_STEM_LOOP_C_5\'GUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00091)
113 +GGUGCGUAGCACC
114 +(((((...)))))
115 +>>__'THE_SOLUTION_STRUCTURE_OF_THE_MAJOR_FAMILY_OF_THE_MUTANT_STEM_LOOP_C_5\'UUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00092)
116 +GGUGCUUAGCACC
117 +(((((...)))))
118 +>>__'THE_SOLUTION_STRUCTURE_OF_THE_MINOR_FAMILY_OF_THE_MUTANT_STEM_LOOP_C_5\'UUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00093)
119 +GGUGCUUAGCACC
120 +(((((...)))))
121 +>>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_TRNA-NEOMYCIN_COMPLEX_'_(PDB_00095)
122 +GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGACUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
123 +(((((((..((((........))))(((((........)))))....(((((.......))))))))))))....
124 +>>__'NMR_STRUCTURE_OF_HCV_IRES_RNA_DOMAIN_IIIC_'_(PDB_00097)
125 +GGGCGUGCCC
126 +(((....)))
127 +>>__'NMR_SOLUTION_STRUCTURE_OF_AN_IN_VITRO_SELECTED_RNA_WHICH_IS_SEQUENCE_SPECIFICALLY_RECOGNIZED_BY_HAMSTER_NUCLEOLIN_RBD12._'_(PDB_00098)
128 +GGCCGAAAUCCCGAAGUAGGCC
129 +((((((..........))))))
130 +>>__'SOLUTION_STRUCTURE_OF_AN_IN_VITRO_SELECTED_RNA_WHICH_IS_SEQUENCE_SPECIFICALLY_RECOGNIZED_BY_RBD12_OF_HAMSTER_NUCLEOLIN.SNRE_(ANTI)_'_(PDB_00099)
131 +GGCCGAAAUCCCGAAGUAGGCC
132 +((((((..........))))))
133 +>>__'SOLUTION_STRUCTURE_OF_AN_RNA_HAIRPIN_FROM_HRV-14_'_(PDB_00100)
134 +GGUACUAUGUACCA
135 +(((((...))))).
136 +>>__'SOLUTION_STRUCTURE_OF_THE_UNMODIFIED_ANTICODON_STEM-LOOP_FROM_E._COLI_TRNA(PHE)_'_(PDB_00103)
137 +GGGGAUUGAAAAUCCCC
138 +(((((((...)))))))
139 +>>__'NMR_STRUCTURE_OF_THE_LP5.1_HAIRPIN_FROM_BACILLUS_RNASE_P_RNA_REFINED_WITH_RESIDUAL_DIPOLAR_COUPLINGS_'_(PDB_00108)
140 +GGCGGUGCUGAGAUGCCCGUC
141 +(((((.((......)))))))
142 +>>__'NMR_STRUCTURE_OF_THE_LP5.1_HAIRPIN_FROM_BACILLUS_RNASE_P_RNA_REFINED_WITHOUT_RESIDUAL_DIPOLAR_COUPLINGS_'_(PDB_00109)
143 +GGCGGUGCUGAGAUGCCCGUC
144 +(((((.((......)))))))
145 +>>__'SOLUTION_STRUCTURE_OF_HIV-1LAI_MUTATED_SL1_HAIRPIN_'_(PDB_00110)
146 +CUUGCUGAAGCACGCACGGCAAG
147 +(((((((.........)))))))
148 +>>__'THE_SOLUTION_STRUCTURE_OF_THE_MUTANT_5\'AUG3\'_TRILOOP_IN_THE_RNA_PROMOTER_REGION_OF_THE_BROME_MOSAIC_VIRUS_GENOMIC_(+)-_RNA_'_(PDB_00114)
149 +GGUGCAUGGCACC
150 +((((.....))))
151 +>>__'STRUCTURE_OF_AGUU_RNA_TETRALOOP,_NMR,_20_STRUCTURES_'_(PDB_00118)
152 +GGUUCAGUUGAACC
153 +(((((....)))))
154 +>>__'NMR_STRUCTURE_OF_A_RIBOSOMAL_RNA_HAIRPIN_CONTAINING_A_CONSERVED_CUCAA_PENTALOOP_'_(PDB_00119)
155 +GGACCCGGGCUCAACCUGGGUCC
156 +((((((((((...))))))))))
157 +>>__'HIV-1(MAL)_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00123)
158 +UUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAU
159 +..(((((..[[[[[[.)))))..(((((((..]]]]]].)))))))..(((((..[[[[[[.)))))..(((((((..]]]]]].)))))))
160 +>>__'CONFORMATION_OF_AN_RNA_PSEUDOKNOT_FROM_MOUSE_MAMMARY_TUMOR_VIRUS,_NMR,_1_STRUCTURE_'_(PDB_00124)
161 +GGCGCAGUGGGCUAGCGCCACUCAAAAGCCCG
162 +((((((..[[[[.))))))........]]]].
163 +>>__'TAR-TAR_"KISSING"_HAIRPIN_COMPLEX_DERIVED_FROM_THE_HIV_GENOME,_NMR,_1_STRUCTURE_'_(PDB_00128)
164 +GAGCCCUGGGAGGCUCGCUGUUCCCAGACAGC
165 +((((([[[[..)))))(((((.]].]])))))
166 +>>__'SOLUTION_STRUCTURE_OF_THE_UNMODIFIED_ANTICODON_STEM-LOOP_FROM_E._COLI_TRNA(PHE)_'_(PDB_00129)
167 +GGGGAUUGAAAAUCCCC
168 +(((((((...)))))))
169 +>>__'STRUCTURE_OF_THE_HISTONE_MRNA_HAIRPIN_REQUIRED_FOR_CELL_CYCLE_REGULATION_OF_HISTONE_GENE_EXPRESSION_'_(PDB_00130)
170 +GGAAGGCCCUUUUCAGGGCCACCC
171 +....((((((....))))))....
172 +>>__'SOLUTION_NMR_STRUCTURE_OF_AN_ANALOG_OF_THE_YEAST_TRNA_PHE_T_STEM_LOOP_CONTAINING_RIBOTHYMIDINE_AT_ITS_NATURALLY_OCCURRING_POSITION_'_(PDB_00131)
173 +CUGUGUUCGAUCCACAG
174 +(((((.......)))))
175 +>>__'A_MUTANT_RNA_PSEUDOKNOT_THAT_PROMOTES_RIBOSOMAL_FRAMESHIFTING_IN_MOUSE_MAMMARY_TUMOR_VIRUS,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00133)
176 +GGCGCAGUGGGCUAGCGCCACUCAAAGGCCCG
177 +(((((...[[[[[.))))).......]]]]].
178 +>>__'PEMV-1_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_15_LOWEST_ENERGY_STRUCTURES_'_(PDB_00134)
179 +UCCGGUCGACUCCGGAGAAACAAAGUCA
180 +(((((..[[[.)))))........]]].
181 +>>__'PEMV-1_P1-P2_FRAMESHIFTING_PSEUDOKNOT_REGULARIZED_AVERAGE_STRUCTURE_'_(PDB_00135)
182 +UCCGGUCGACUCCGGAGAAACAAAGUCA
183 +(((((..[[..))))).........]].
184 +>>__'ATOMIC_RESOLUTION_CRYSTAL_STRUCTURE_OF_A_VIRAL_RNA_PSEUDOKNOT_'_(PDB_00138)
185 +GGCGCGGCACCGUCCGCGGAACAAACGG
186 +..(((((..[[[.))))).......]]]
187 +>>__'LOW_RESOLUTION_CRYSTAL_STRUCTURE_OF_A_VIRAL_RNA_PSEUDOKNOT_'_(PDB_00139)
188 +GGCGCGGCACCGUCCGCGGAACAAACGG
189 +..(((((..[[[.))))).......]]]
190 +>>__'SOLUTION_STRUCTURE_OF_THE_U6_INTRAMOLECULAR_STEM-LOOP_RNA_'_(PDB_00141)
191 +GGUUCCCCUGCAUAAGGAUGAACC
192 +((((((((((...))))).)))))
193 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_YEAST_TRNA-PHE_WITH_4_MODIFICATIONS_(OMC32_OMG34_1MG37_5MC40)_'_(PDB_00147)
194 +CCAGACUGAAGAUCUGG
195 +((((((.....))))))
196 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_YEAST_TRNA-PHE_WITH_3_MODIFICATIONS_(OMC32_OMG34_M5C40)_'_(PDB_00148)
197 +CCAGACUGAAGAUCUGG
198 +((((((.....))))))
199 +>>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_26MER_RNA_MOLECULE,_REPRESENTING_A_NEW_RNA_MOTIF,_THE_HOOK-TURN_'_(PDB_00155)
200 +CCAUGCGAACCGCGAUCCUAGUGUGG
201 +((((((((..........))))))))
202 +>>__'STRUCTURE_OF_23S_RIBOSOMAL_RNA_HAIRPIN_35_'_(PDB_00160)
203 +GGCGUAACGUUGAAAAGUUACGCC
204 +(((((((((......)))))))))
205 +>>__'SOLUTION_STRUCTURE_OF_B._SUBTILIS_T_BOX_ANTITERMINATOR_RNA_'_(PDB_00168)
206 +GAGGGUGGAACCGCGCGCGUCCCUC
207 +((((........((....)).))))
208 +>>__'SOLUTION_STRUCTURE_OF_THE_P2B_HAIRPIN_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00171)
209 +GGGCUGUUUUUCUCGCUGACUUUCAGCCCC
210 +((((((((((((.....)))))))))))).
211 +>>__'IRON_RESPONSIVE_ELEMENT_RNA_HAIRPIN,_NMR,_15_STRUCTURES_'_(PDB_00172)
212 +GGAGUGCUUCAACAGUGCUUGGACGCUCC
213 +((((((.(((((......)))))))))))
214 +>>__'U80G_U6_INTRAMOLECULAR_STEM-LOOP_RNA_FROM_SACCHAROMYCES_CEREVISIAE_'_(PDB_00173)
215 +GGUUCCCCUGCAUAAGGAGGAACC
216 +((((((((((...)))).))))))
217 +>>__'SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM-LOOP_CONTAINING_AN_SP_PHOSPHOROTHIOATE_AT_NUCLEOTIDE_U80_'_(PDB_00177)
218 +GGUUCCCCUGCAUAAGGAUGAACC
219 +((((((((((...))))).)))))
220 +>>__'P6.1_STEM_LOOP_FROM_THE_ACTIVATION_DOMAIN_OF_HTR_'_(PDB_00180)
221 +GAGAGUUGGGCUCUC
222 +((((((...))))))
223 +>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_IIB_'_(PDB_00184)
224 +GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC
225 +(((((((((((((.......))))))).))))))
226 +>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_II_'_(PDB_00185)
227 +GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC
228 +(((((.((((.....((((((.((((((((..(((((.......)))))...)))))))).)).)))))))))))))
229 +>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_II_(MINIMIZED_AVERAGE_STRUCTURE)_'_(PDB_00186)
230 +GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC
231 +(((((.((((.....((((((((((((((((((((((.......))))))).))))))))))).)))))))))))))
232 +>>__'SOLUTION_STRUCTURE_OF_THE_DYSKERATOSIS_CONGENITA_MUTANT_P2B_HAIRPIN_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00191)
233 +GGCUCUCAGUGAGCC
234 +(((((.....)))))
235 +>>__'NMR_STRUCTURE_OF_TAU_EXON_10_SPLICING_REGULATORY_ELEMENT_RNA_'_(PDB_00197)
236 +GGCAGUGUGAGUACCUUCACACGUC
237 +....(((((((....)))))))...
238 +>>__'NMR_STRUCUTRE_OF_5\'-R(GGACACGAAAUCCCGAAGUAGUGUCC)-3\'_:_AN_RNA_HAIRPIN_CONTAINING_THE_IN_VITRO_SELECTED_CONSENSUS_SEQUENCE_FOR_NUCLEOLIN_RBD12_'_(PDB_00201)
239 +GGACACGAAAUCCCGAAGUAGUGUCC
240 +((((((((((.....)).))))))))
241 +>>__'24-MER_RNA_HAIRPIN_COAT_PROTEIN_BINDING_SITE_FOR_BACTERIOPHAGE_R17_(NMR,_MINIMIZED_AVERAGE_STRUCTURE)_'_(PDB_00206)
242 +GGGACUGACGAUCACGCAGUCUAU
243 +.((((((.((....))))))))..
244 +>>__'THE_STRUCTURE_OF_AN_RNA_PSEUDOKNOT_THAT_CAUSES_EFFICIENT_FRAMESHIFTING_IN_MOUSE_MAMMARY_TUMOR_VIRUS_'_(PDB_00209)
245 +GGCGCAGUGGGCUAGCGCCACUCAAAAGGCCCAU
246 +[[[[[..((((((.]]]]]........)))))).
247 +>>__'FIRST_STEM_LOOP_OF_THE_SL1_RNA_FROM_CAENORHABDITIS_ELEGANS,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00216)
248 +UUACCCAAGUUUGAGGUAA
249 +(((((((....)).)))))
250 +>>__'FIRST_STEM_LOOP_OF_THE_SL1_RNA_FROM_CAENORHABDITIS_ELEGANS,_NMR,_16_STRUCTURES_'_(PDB_00217)
251 +UUACCCAAGUUUGAGGUAA
252 +(((((((....)).)))))
253 +>>__'REFINED_SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM_LOOP_(ISL)_RNA_USING_RESIDUAL_DIPOLAR_COUPLINGS_(RDCS)_'_(PDB_00218)
254 +GGUUCCCCUGCAUAAGGAUGAACC
255 +((((((((((...))))).)))))
256 +>>__'SOLUTION_STRUCTURE_OF_ITALY1_("INITIATOR_TRNA_ANTICODON_LOOP_FROM_YEAST"),_AN_UNMODIFIED_21-NT_RNA_WITH_THE_SEQUENCE_OF_THE_ANTICODON_STEM-LOOP_OF_YEAST_INITIATOR_TRNA_'_(PDB_00219)
257 +GGCAGGGCUCAUAACCCUGCC
258 +(((((((.......)))))))
259 +>>__'STEM_LOOP_IIA_FROM_U2SNRNA_OF_SACCHAROMYCES_CEREVISIAE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00224)
260 +GGUCAGUGUAACAACUGACC
261 +((((((((....))))))))
262 +>>__'STRUCTURE_OF_AN_RNA_HAIRPIN_LOOP_WITH_A_5\'-CGUUUCG-3\'_LOOP_MOTIF_BY_HETERONUCLEAR_NMR_SPECTROSCOPY_AND_DISTANCE_GEOMETRY,_15_STRUCTURES_'_(PDB_00225)
263 +GGCGUACGUUUCGUACGCC
264 +(((((((.....)))))))
265 +>>__'CONSERVED_RNA_COMPONENT_OF_THE_PEPTIDYL_TRANSFERASE_CENTER,_NMR,_33_STRUCTURES_'_(PDB_00226)
266 +GACUGGGGCGGUC
267 +(((((...)))))
268 +>>__'YEAST_INITIATOR_TRNA_'_(PDB_00229)
269 +AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA
270 +(((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))))....
271 +>>__'GAAA_RNA_TETRALOOP,_NMR,_10_STRUCTURES_'_(PDB_00231)
272 +GGGCGAAAGCCU
273 +(((......)))
274 +>>__'SOLUTION_NMR_STRUCTURE_OF_A_SUBSTRATE_FOR_THE_ARCHAEAL_PRE-_TRNA_SPLICING_ENDONUCLEASES:_THE_BULGE-HELIX-BULGE_MOTIF,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00240)
275 +GGGUGACUCCAGAGGUCGAGAGACCGGAGAUAUCACCC
276 +((((((((((...((((....))))))))...))))))
277 +>>__'RNA_LOOP-LOOP_COMPLEX:_THE_COLE1_INVERTED_LOOP_SEQUENCE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00241)
278 +GGCAACGGAUGGUUCGUUGCCGCACCGAACCAUCCGGUGC
279 +((((((([[[[[[[)))))))((((((]]]]]]]))))))
280 +>>__'AN_INVESTIGATION_OF_THE_STRUCTURE_OF_THE_PSEUDOKNOT_WITHIN_THE_GENE_32_MESSENGER_RNA_OF_BACTERIOPHAGE_T2_USING_HETERONUCLEAR_NMR_METHODS_'_(PDB_00243)
281 +GCUGACCAGCUAUGAGGUCAUACAUCGUCAUAGCAC
282 +..[[[[[.(((((((]]]]].......)))))))..
283 +>>__'STEM_LOOP_IIA_FROM_U2_SNRNA_OF_SACCHAROMYCES_CEREVISIAE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00245)
284 +GGUCAGUGUAACAACUGACC
285 +((((((((....))))))))
286 +>>__'RNA_PSEUDOKNOT_WITH_3D_DOMAIN_SWAPPING_'_(PDB_00256)
287 +UCCGAAGUGCAACGGGAAAAUGCACU
288 +.((((......))))...........
289 +>>__'STRUCTURE_OF_THE_3\'_HAIRPIN_OF_THE_TYMV_PSEUDOKNOT:_PREFORMATION_IN_RNA_FOLDING_'_(PDB_00258)
290 +GGUUCCGAGGGUCAUCGGAACCA
291 +((((((((......)))))))).
292 +>>__'CRYSTAL_STRUCTURE_OF_AN_RNA_PSEUDOKNOT_FROM_BEET_WESTERN_YELLOW_VIRUS_INVOLVED_IN_RIBOSOMAL_FRAMESHIFTING_'_(PDB_00269)
293 +GGCGCGGCACCGUCCGCGGAACAAACGG
294 +..(((((..[[[.))))).......]]]
295 +>>__'STRUCTURE_OF_THE_HIV-1_NUCLEOCAPSID_PROTEIN_BOUND_TO_THE_SL3_PSI-RNA_RECOGNITION_ELEMENT,_NMR,_25_STRUCTURES_'_(PDB_00285)
296 +GGACUAGCGGAGGCUAGUCC
297 +((((((((....))))))))
298 +>>__'SATELLITE_TOBACCO_MOSAIC_VIRUS/RNA_COMPLEX_'_(PDB_00286)
299 +AAAAAAAAAAUUUUUUUUUU
300 +..((((((...))))))...
301 +>>__'LOOP_D/LOOP_E_ARM_OF_ESCHERICHIA_COLI_5S_RRNA,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00288)
302 +GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
303 +(((((((((((((((((((...)))))))))))))))))))
304 +>>__'SOLUTION_STRUCTURE_OF_PHAGE_P22_N_PEPTIDE-BOX_B_RNA_COMPLEX,_NMR,_20_STRUCTURES_'_(PDB_00289)
305 +GCGCUGACAAAGCGC
306 +((((((...))))))
307 +>>__'CRYSTAL_STRUCTURE_OF_THE_SPLICEOSOMAL_U2B\'\'-U2A\'_PROTEIN_COMPLEX_BOUND_TO_A_FRAGMENT_OF_U2_SMALL_NUCLEAR_RNA_'_(PDB_00293)
308 +CCUGGUAUUGCAGUACCUCCAGGUCCUGGUAUUGCAGUACCUCCAGGU
309 +((((((...........)))))).((((((...........)))))).
310 +>>__'HIV-2_TRANS_ACTIVATING_REGION_RNA_COMPLEX_WITH_ARGININAMIDE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00299)
311 +GGCCAGAUUGAGCCUGGGAGCUCUCUGGCC
312 +(((((((..((((......)))))))))))
313 +>>__'BACTERIOPHAGE_MS2_CAPSID_PROTEIN/RNA_COMPLEX_'_(PDB_00303)
314 +AUGAGGAUUACCCAUGUGAGGAUUACCC
315 +(((.((....)))))....((....)).
316 +>>__'STRUCTURE_OF_A_MS2_COAT_PROTEIN_MUTANT_IN_COMPLEX_WITH_AN_RNA_OPERATOR_'_(PDB_00304)
317 +AUGAGGAUUACCCAUGAUGAGGAUUACCCA
318 +(((.((....)))))..((.((....))))
319 +>>__'ARG-BOUND_TAR_RNA,_NMR_'_(PDB_00306)
320 +GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
321 +..((((...((((......))))))))..
322 +>>__'U1A-UTRRNA,_NMR,_31_STRUCTURES_'_(PDB_00312)
323 +GGCAGAGUCCUUCGGGACAUUGCACCUGCC
324 +(((((.((((....)))).......)))))
325 +>>__'BOVINE_IMMUNODEFICIENCY_VIRUS_TAT-TAR_COMPLEX,_NMR,_5_STRUCTURES_'_(PDB_00317)
326 +GGCUCGUGUAGCUCAUUAGCUCCGAGCC
327 +((((((...((((....)))).))))))
328 +>>__'HEPATITIS_DELTA_VIRUS_RIBOZYME_'_(PDB_00335)
329 +GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
330 +(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
331 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_5S_RRNA_E-LOOP/L25_COMPLEX_'_(PDB_00339)
332 +GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC
333 +.((((((((((((((((....))))))))))))))))
334 +>>__'CRYSTAL_STRUCTURE_OF_E.COLI_RIBOSOMAL_PROTEIN_L25_COMPLEXED_WITH_A_5S_RRNA_FRAGMENT_AT_1.8_A_RESOLUTION_'_(PDB_00341)
335 +CCCAUGCGAGAGUAGGGACUGCCGAUGGUAGUGUGGGG
336 +((((((((((((((((.....)))))))))))))))).
337 +>>__'U1A_SPLICEOSOMAL_PROTEIN/HEPATITIS_DELTA_VIRUS_GENOMIC_RIBOZYME_COMPLEX_'_(PDB_00346)
338 +GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
339 +(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
340 +>>__'CORE_OF_THE_ALU_DOMAIN_OF_THE_MAMMALIAN_SRP_'_(PDB_00352)
341 +GGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC
342 +(((((((((((((..[[))))))))....((((.]].....)))))))))
343 +>>__'CRYSTAL_STRUCTURE_OF_NOVA-2_KH3_K-HOMOLOGY_RNA-BINDING_DOMAIN_BOUND_TO_20-MER_RNA_HAIRPIN_'_(PDB_00357)
344 +GAGGACCUAGAUCACCCCUCGAGGACCUAGAUCACCCCUC
345 +(((((..........)))))(((((..........)))))
346 +>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_THE_RNA_MAJOR_GROOVE_IN_THE_TAU_EXON_10_SPLICING_REGULATORY_ELEMENT_BY_AMINOGLYCOSIDE_ANTIBIOTICS_'_(PDB_00361)
347 +GGCAGUGUGAGUACCUUCACACGUC
348 +....((((((......))))))...
349 +>>__'THE_CRYSTAL_STRUCTURE_OF_PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_COGNATE_TRNAPHE_'_(PDB_00362)
350 +GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
351 +(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
352 +>>__'CRYSTAL_STRUCTURE_OF_GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA-GLN_MUTANT_AND_AN_ACTIVE-SITE_INHIBITOR_'_(PDB_00373)
353 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
354 +((((((..((((.......))))((((((((...))))))))..(((((.......))))))))))).....
355 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA_MUTANT_AND_AN_ACTIVE_SITE_INHIBITOR_'_(PDB_00374)
356 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
357 +((((((..((((.......))))((((((((...))))))))...(((((.......))))))))))).....
358 +>>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376)
359 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA
360 +((((((..(((.........)))((((((((...))))))))...(((((.......))))))))))).....
361 +>>__'SOLUTION_STRUCTURE_OF_HTLV-1_PEPTIDE_BOUND_TO_ITS_RNA_APTAMER_TARGET_'_(PDB_00377)
362 +GGGCGCCGGUACGCAAGUACGACGGUACGCUCC
363 +((((((((((((....))))..)))..))))).
364 +>>__'NMR_STRUCTURE_OF_THE_HIV-1_NUCLEOCAPSID_PROTEIN_BOUND_TO_STEM-LOOP_SL2_OF_THE_PSI-RNA_PACKAGING_SIGNAL._IMPLICATIONS_FOR_GENOME_RECOGNITION_'_(PDB_00383)
365 +GGCGACUGGUGAGUACGCC
366 +(((((((....)).)))))
367 +>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00402)
368 +GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
369 +(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
370 +>>__'SOLUTION_STRUCTURE_OF_NUCLEOLIN_RBD12_IN_COMPLEX_WITH_SNRE_RNA_'_(PDB_00407)
371 +GGCCGAAAUCCCGAAGUAGGCC
372 +((((((..........))))))
373 +>>__'COMPLEX_OF_HIV-1_RRE-IIB_RNA_WITH_RSG-1.2_PEPTIDE_'_(PDB_00420)
374 +GGUCUGGGCGCACUUCGGUGACGGUACAGGCC
375 +...((((((((((....))).))).))))...
376 +>>__'STRUCTURAL_BASIS_OF_ANTICODON_LOOP_RECOGNITION_BY_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00425)
377 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
378 +((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
379 +>>__'STRUCTURAL_BASIS_FOR_TRANSFER_RNA_AMINOACEYLATION_BY_ESCHERICHIA_COLI_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00426)
380 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
381 +((((((..(((.........))).(((((((...))))))).....(((((.......))))))))))).....
382 +>>__'BACTERIOPHAGE_HK022_NUN-PROTEIN-NUTBOXB-RNA_COMPLEX_'_(PDB_00434)
383 +GCCCUGAAAAAGGGC
384 +((((((...))))))
385 +>>__'CRYSTAL_STRUCTURE_OF_ARCHAEAL_TYROSYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA(TYR)_AND_L-TYROSINE_'_(PDB_00474)
386 +CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA
387 +(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).
388 +>>__'CRYSTAL_STRUCTURE_OF_THE_RIBOTOXIN_RESTRICTOCIN_AND_A_31-_MER_SRD_RNA_INHIBITOR_'_(PDB_00481)
389 +GCGCUCCUCAGUACGAGAGGAACCGGAGCGCGCGCUCCUCAGUACGAGAGGAACCGGAGCGC
390 +((((((((((.(((....)))))))))))))((((((((((.(((....)))))))))))))
391 +>>__'CRYSTAL_STRUCTURE_OF_RIBOTOXIN_RESTRICTOCIN_AND_A_29-MER_SRD_RNA_ANALOG_'_(PDB_00482)
392 +CGCUCCUCAGUACGAUAGGAACCGGAGCGCGCUCCUCAGUACGAUAGGAACCGGAGCG
393 +(((((((((.(((....))))))))))))(((((((((.(((....))))))))))))
394 +>>__'CRYSTAL_STRUCTURE_OF_RIBOTOXIN_RESTRICTOCIN_COMPLEXED_WITH_A_29-MER_SARCIN/RICIN_DOMAIN_RNA_ANALOG_'_(PDB_00483)
395 +CGCUCCUCAGUACGAGAGGAACCGGAGCGCGCUCCUCAGUACGAGAGGAACCGGAGCG
396 +(((((((((.(((....))))))))))))(((((((((.(((....))))))))))))
397 +>>__'HUMAN_SRP19_IN_COMPLEX_WITH_HELIX_6_OF_HUMAN_SRP_RNA_'_(PDB_00487)
398 +GGUGACCUCCCGGGAGCGGGGGACCACUA
399 +((((((((((((....)))))))))))).
400 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_RNA_HAIRPIN_BINDING_SITE_FOR_THE_HISTONE_STEM-LOOP_BINDING_PROTEIN_'_(PDB_00495)
401 +GGCCCUUUUCAGGGCC
402 +((((((....))))))
403 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_RNA_HAIRPIN_BINDING_SITE_FOR_THE_HISTONE_STEM-LOOP_BINDING_PROTEIN_'_(PDB_00497)
404 +GGCCCUUUUCAGGGCC
405 +....((....))....
406 +>>__'CRYSTAL_STRUCTURE_OF_THE_E._COLI_PSEUDOURIDINE_SYNTHASE_TRUB_BOUND_TO_A_T_STEM-LOOP_RNA_'_(PDB_00513)
407 +GGCAACGGUUCGAUCCCGUUGC
408 +.(((((((.......)))))))
409 +>>__'RNA_APTAMER_COMPLEXED_WITH_ARGININE,_NMR_'_(PDB_00526)
410 +AGAAGGAGCGUACAGGUAGGUCGCU
411 +.....(((...........)))...
412 +>>__'CRYSTAL_STRUCTURE_OF_T3C_MUTANT_S15_RIBOSOMAL_PROTEIN_IN_COMPLEX_WITH_16S_RRNA_'_(PDB_00535)
413 +GGGCGGCCUUCGGGCUAGACGGUGGGAGAGGCUUCGGCUGGUCCACCCGUGACGCUC
414 +((((.(((....)))...((((((((((.(((....)))))))))).)))...))))
415 +>>__'CRYSTAL_STRUCTURE_OF_THE_SRP19-7S.S_SRP_RNA_COMPLEX_OF_M._JANNASCHII_'_(PDB_00547)
416 +UCGGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUC
417 +..((((..(((((.(((((((((....)))))))))..)))))....((((((((....((((.(((((....))))).)))).)))))))).))))
418 +>>__'STRUCTURE_OF_TAR_RNA_COMPLEXED_WITH_A_TAT-TAR_INTERACTION_NANOMOLAR_INHIBITOR_THAT_WAS_IDENTIFIED_BY_COMPUTATIONAL_SCREENING_'_(PDB_00553)
419 +GGCCAGAUCUGAGCCUGGGAGCUCUCUGGCC
420 +(((((((...((((......)))))))))))
421 +>>__'DETAILED_ANALYSIS_OF_RNA-PROTEIN_INTERACTIONS_WITHIN_THE_BACTERIAL_RIBOSOMAL_PROTEIN_L5/5S_RRNA_COMPLEX_'_(PDB_00570)
422 +GGCACCUGACCCCAUGCCGAACUCAGAAGUGCCCGGCACCUGACCCCAUGCCGAACUCAGAAGUGCCC
423 +(((((((((....((....)).))))..))))).(((((((((....((....)).))))..))))).
424 +>>__'BIV_TAT_PEPTIDE_(RESIDUES_68-81),_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00574)
425 +GGCUCGUGUAGCUCAUUAGCUCCGAGCC
426 +((((((...((((....)))).))))))
427 +>>__'LAMBDA3_ELONGATION_COMPLEX_WITH_FOUR_PHOSPHODIESTER_BOND_FORMED_'_(PDB_00588)
428 +GGGGGUAGCCCCCCCC
429 +.((.......))....
430 +>>__'REOVIRUS_POLYMERASE_LAMBDA3_ELONGATION_COMPLEX_WITH_ONE_PHOSPHODIESTER_BOND_FORMED_'_(PDB_00590)
431 +GCUUAGCUCC
432 +((...))...
433 +>>__'SACCHARIDE-RNA_RECOGNITION_IN_THE_NEOMYCIN_B_/_RNA_APTAMER_COMPLEX_'_(PDB_00603)
434 +GGACUGGGCGAGAAGUUUAGUCC
435 +((((((((((...))))))))))
436 +>>__'SOLUTION_STRUCTURE_OF_THE_BACTERIOPHAGE_PHI21_N_PEPTIDE-_BOXB_RNA_COMPLEX_'_(PDB_00617)
437 +GGUUCACCUCUAACCGGGUGAGCC
438 +((((((((((....))))))))))
439 +>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMINE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00620)
440 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
441 +((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))).....
442 +>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMATE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00621)
443 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
444 +((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
445 +>>__'MODEL_FOR_THIOSTREPTON_ANTIBIOTIC_BINDING_TO_L11_SUBSTRATE_FROM_50S_RIBOSOMAL_RNA_'_(PDB_00627)
446 +GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
447 +(((((((((..((((.......))))..)))........((((....)))).))))))
448 +>>__'CRYSTAL_STRUCTURE_OF_THE_TRNA_DOMAIN_OF_TRANSFER-MESSENGER_RNA_IN_COMPLEX_WITH_SMPB_'_(PDB_00637)
449 +GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGCUCGACGGGGACUUCGGUCCUCGGA
450 +......((((((((....))))))))..(((((.......)))))...((((((((....)))))))).
451 +>>__'CHEMICAL_TRAPPING_AND_CRYSTAL_STRUCTURE_OF_A_CATALYTIC_TRNA_GUANINE_TRANSGLYCOSYLASE_COVALENT_INTERMEDIATE_'_(PDB_00648)
452 +AGCACGGCUUAAACCGUGCAGCACGGCUUAAACCGUGCUUUU
453 +(((((((......)))))))((((((......))))))....
454 +>>__'CHEMICAL_TRAPPING_AND_CRYSTAL_STRUCTURE_OF_A_CATALYTIC_TRNA_GUANINE_TRANSGLYCOSYLASE_COVALENT_INTERMEDIATE_'_(PDB_00649)
455 +AGCACGGCUGUAAACCGUGCAGCACGGCUUAAACCGUGC
456 +(((((((.......)))))))((((((......))))))
457 +>>__'HIV-1_TAR_RNA/NEOMYCIN_B_COMPLEX_'_(PDB_00664)
458 +GCCAGAUUUGAGCCUGGGAGCUCUCUGGC
459 +((((((...((((......))))))))))
460 +>>__'BACTERIOPHAGE_LAMBDA_N-PROTEIN-NUTBOXB-RNA_COMPLEX_'_(PDB_00668)
461 +GCCCUGAAAAAGGGC
462 +((((((...))))))
463 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235N_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00669)
464 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
465 +((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
466 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235G_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00670)
467 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
468 +((((((..(((.........)))(((((((.....)))))))....(((((.......))))))))))).....
469 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_I129T_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00671)
470 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
471 +((((((..(((.........)))((((((.......))))))....(((((.......))))))))))).....
472 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA_AND_AN_AMINO_ACID_ANALOG_'_(PDB_00672)
473 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
474 +((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
475 +>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00673)
476 +GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
477 +(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
478 +>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00674)
479 +GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
480 +(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
481 +>>__'SOLUTION_STRUCTURE_OF_THE_COMPLEX_FORMED_BY_THE_TWO_N-_TERMINAL_RNA-BINDING_DOMAINS_OF_NUCLEOLIN_AND_A_PRE-RRNA_TARGET_'_(PDB_00691)
482 +GGAUGCCUCCCGAGUGCAUCC
483 +((((((.........))))))
484 +>>__'THE_STRUCTURE_OF_A_RIBOSOMAL_PROTEIN_S8/SPC_OPERON_MRNA_COMPLEX_'_(PDB_00702)
485 +GGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCCGGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCC
486 +((((((.((.((..((((((((......)))))).))))))))))))((((((.((.((..((((((((......)))))).))))))))))))
487 +>>__'AVERAGE_SOLUTION_STRUCTURE_OF_A_PSEUDO-5\'-SPLICE_SITE_FROM_THE_NEGATIVE_REGULATOR_OF_SPLICING_OF_ROUS_SARCOMA_VIRUS_'_(PDB_00705)
488 +GGGGAGUGGUUUGUAUCCUUCCC
489 +((((((.((......))))))))
490 +>>__'SOLUTION_STRUCTURE_OF_RESIDUES_907-929_FROM_ROUS_SARCOMA_VIRUS_'_(PDB_00706)
491 +GGGGAGUGGUUUGUAUCCUUCCC
492 +((((((.(((....)))))))))
493 +>>__'HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_MG2+_BOUND_'_(PDB_00714)
494 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
495 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
496 +>>__'CRYSTAL_STRUCTURE_OF_A_C75U_MUTANT_HEPATITIS_DELTA_VIRUS_RIBOZYME_PRECURSOR,_IN_CU2+_SOLUTION_'_(PDB_00715)
497 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
498 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
499 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_COBALT_HEXAMMINE_SOLUTION_'_(PDB_00716)
500 +AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
501 +..(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
502 +>>__'SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM_LOOP_(ISL)_RNA_AT_PH_5.7_'_(PDB_00721)
503 +GGUUCCCCUGCAUAAGGAUGAACC
504 +((((((((((...))))).)))))
505 +>>__'HIGH_RESOLUTION_STRUCTURE_OF_A_PICORNAVIRAL_INTERNAL_CIS-_ACTING_REPLICATION_ELEMENT_'_(PDB_00727)
506 +GGUCAUCGUUGAGAAAACGAAACAGACGGUGGCC
507 +((..(((((................)))))..))
508 +>>__'NMR_STRUCTURE_OF_THE_VS_RIBOZYME_STEM-LOOP_V_RNA_IN_THE_ABSENCE_OF_MULTIVALENT_IONS._'_(PDB_00730)
509 +GCGAGUUGACUACUCGC
510 +((((((.....))))))
511 +>>__'SACCHARIDE-RNA_RECOGNITION_IN_AN_AMINOGLYCOSIDE_ANTIBIOTIC-_RNA_APTAMER_COMPLEX,_NMR,_7_STRUCTURES_'_(PDB_00737)
512 +GGCACGAGGUUUAGCUACACUCGUGCC
513 +(((((((((((....))).))))))))
514 +>>__'CRYSTAL_STRUCTURE_OF_CYSTEINYL-TRNA_SYNTHETASE_BINARY_COMPLEX_WITH_TRNACYS_'_(PDB_00742)
515 +GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA
516 +(((((((..(((.........))).((((((.....))))))....(((((.......))))))))))))....
517 +>>__'CRYSTAL_STRUCTURE_OF_A_COMPLEX_BETWEEN_WT_BACTERIOPHAGE_MS2_COAT_PROTEIN_AND_AN_F5_APTAMER_RNA_STEMLOOP_WITH_2AMINOPURINE_SUBSTITUTED_AT_THE-10_POSITION_'_(PDB_00743)
518 +CCGGGGGAUCACCACGGCGGGGGAUCACCACGG
519 +((((.((....))))))(((.((....))))).
520 +>>__'THE_STRUCTURE_OF_A_RIBOSOMAL_PROTEIN_L1-MRNA_COMPLEX_'_(PDB_00746)
521 +GGGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCCGGGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCC
522 +.(((((((((((((((((((....)))).)))))....))))))))))..(((((((((((((((((((....)))).)))))....)))))))))).
523 +>>__'GUANINE_RIBOSWITCH_BOUND_TO_HYPOXANTHINE_'_(PDB_00749)
524 +GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCC
525 +(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..)))))))
526 +>>__'REOVIRUS_POLYMERASE_LAMBDA-3_LOCALIZED_BY_ELECTRON_CRYOMICROSCOPY_OF_VIRIONS_AT_7.6-A_RESOLUTION_'_(PDB_00753)
527 +GGGGGUAGCCCCCCCC
528 +.((.......))....
529 +>>__'U1A_MUTANT/RNA_COMPLEX_+_GLYCEROL_'_(PDB_00754)
530 +AAUCCAUUGCACGGAUUAAUCCAUUGCACUCCGGAUUUAAUCCAUUGCACGGAUU
531 +.((((.......)))).(((((..........)))))...(((.......)))..
532 +>>__'DESIGNED_HIV-1_TAR_BINDING_LIGAND_'_(PDB_00755)
533 +GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
534 +((((((...((((......))))))))))
535 +>>__'NMR_STRUCTURE_OF_A_SYNTHETIC_SMALL_MOLECULE,_RBT203,_BOUND_TO_HIV-1_TAR_RNA_'_(PDB_00756)
536 +GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
537 +((((((...((((......))))))))))
538 +>>__'NMR_STRUCTURE_OF_A_SYNTHETIC_SMALL_MOLECULE,_RBT158,_BOUND_TO_HIV-1_TAR_RNA_'_(PDB_00757)
539 +GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
540 +((((((...((((......))))))))))
541 +>>__'THE_STRUCTURAL_BASIS_FOR_RNA_SPECIFICITY_AND_CA2_INHIBITION_OF_AN_RNA-DEPENDENT_RNA_POLYMERASE_PHI6P2_CA2+_INHIBITION_COMPLEX_'_(PDB_00759)
542 +UUCCUUCCUUCCGGGGGG
543 +..((..[[..{{))]]}}
544 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_EDTA_SOLUTION_'_(PDB_00760)
545 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
546 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
547 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_AND_MN2+_BOUND_'_(PDB_00761)
548 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
549 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
550 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_BA2+_SOLUTION_'_(PDB_00762)
551 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
552 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
553 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_IMIDAZOLE_AND_SR2+_SOLUTION_'_(PDB_00763)
554 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
555 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
556 +>>__'CRYSTAL_STRUCTURE_OF_THE_WILD_TYPE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_IN_EDTA_SOLUTION_'_(PDB_00764)
557 +GGCCGGCAUGGUCCCAGCCUCCUCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
558 +(((((((....[[[[[(((.[[...))))))))))]]...(((((..........)))))....]]]]].
559 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRODUCT_WITH_C75U_MUTAION,_CLEAVED_IN_IMIDAZOLE_AND_MG2+_SOLUTIONS_'_(PDB_00765)
560 +GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
561 +(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
562 +>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_SR2+_SOLUTION_'_(PDB_00766)
563 +AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
564 +..(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
565 +>>__'CRYSTAL_STRUCTURE_OF_TRNA_NUCLEOTIDYLTRANSFERASE_COMPLEXED_WITH_A_PRIMER_TRNA_AND_AN_INCOMING_ATP_ANALOG_'_(PDB_00767)
566 +GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCGGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACCAA
567 +(((((((.(((.........))).)))))))(((((((.(((.........))).))))))).....
568 +>>__'SOLUTION_STRUCTURE_OF_AN_RNA_STEM-LOOP_DERIVED_FROM_THE_3\'_CONSERVED_REGION_OF_EEL_LINE_UNAL2_'_(PDB_00798)
569 +GGCUUUGGAUAAAAGCC
570 +(((((((...)))))))
571 +>>__'SOLUTION_STRUCTURE_OF_THE_EXTENDED_U6_ISL_AS_OBSERVED_IN_THE_U2/U6_COMPLEX_FROM_SACCHAROMYCES_CEREVISIAE_'_(PDB_00809)
572 +GAGCAGUUCCCCUGCAUAAGGAUGAACCGUUC
573 +((((((((((((((...))))).)))))))))
574 +>>__'THE_STRUCTURE_OF_A_RIGOROUSLY_CONSERVED_RNA_ELEMENT_WITHIN_THE_SARS_VIRUS_GENOME_'_(PDB_00810)
575 +GGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
576 +..((((((((...(((((((((...)))..)).))))..))))))))
577 +>>__'HIV-1_SUBTYPE_F_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00816)
578 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
579 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
580 +>>__'HIV-1_SUBTYPE_B_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00817)
581 +CUUGCUGAAGCGCGCACGGCAAGCUUGCUGAAGCGCGCACGGCAAG
582 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
583 +>>__'HIV-1_SUBTYPE_A_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00818)
584 +CUUGCUGAGGUGCACACAGCAAGCUUGCUGAGGUGCACACAGCAAG
585 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
586 +>>__'SOLUTION_STRUCTURE_OF_AUCGCA_LOOP_'_(PDB_00825)
587 +GGAGAUCGCACUCCA
588 +(((((....))))).
589 +>>__'A-RIBOSWITCH-ADENINE_COMPLEX_'_(PDB_00828)
590 +CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG
591 +(((((((((...(((((((.[[[.[[)))))))........((((((]]..]]]))))))..)))))))))
592 +>>__'G-RIBOSWITCH-GUANINE_COMPLEX_'_(PDB_00829)
593 +GGAUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGGUC
594 +.(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..)))))))
595 +>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MN_SOAKED_'_(PDB_00831)
596 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
597 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
598 +>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MPD_FORM_'_(PDB_00832)
599 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
600 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
601 +>>__'SOLUTION_STRUCTURE_OF_THE_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_20_LOWEST_ENERGY_STRUCTURES_'_(PDB_00842)
602 +AGUGGCGCCGACCACUUAAAAACACCGG
603 +(((((..[[[.))))).........]]]
604 +>>__'SOLUTION_STRUCTURE_OF_THE_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_REGULARIZED_AVERAGE_STRUCTURE_'_(PDB_00843)
605 +AGUGGCGCCGACCACUUAAAAACACCGG
606 +(((((..[[[.))))).........]]]
607 +>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00855)
608 +GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC
609 +((((((.((((........))))..))))))
610 +>>__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857)
611 +GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA
612 +[[[[[[........(((((((((]]]]]]........))))))))).
613 +>>__'SOLUTION_STRUCTURE_OF_THE_VS_RIBOZYME_STEM-LOOP_V_IN_THE_PRESENCE_OF_MGCL2_'_(PDB_00858)
614 +GCGAGUUGACUACUCGC
615 +((((((.....))))))
616 +>>__'SOLUTION_STRUCTURE_OF_THE_NEUROSPORA_VS_RIBOZYME_STEM-LOOP_V_IN_THE_PRESENCE_OF_MGCL2_WITH_MODELING_OF_BOUND_MANGANESE_IONS_'_(PDB_00859)
617 +GCGAGUUGACUACUCGC
618 +((((((.....))))))
619 +>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00860)
620 +GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC
621 +(((((((((((........)))).)))))))
622 +>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00861)
623 +GGAUAUAUGAUAUAAUUUGAUCAGUAUAUCC
624 +((((((.((((........))))..))))))
625 +>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00862)
626 +GGAUAUAUGAUAUAAUUUGAUCAGUAUAUCC
627 +((((((.((((........))))..))))))
628 +>>__'SOLUTION_STRUCTURE_OF_THE_CENTRAL_REGION_OF_THE_HUMAN_GLUR-_B_R/G_PRE-MRNA_'_(PDB_00865)
629 +GGUAACAAUAUGCUAAAUGUUGUUACC
630 +((((((((((((...))))))))))))
631 +>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_UUUOH_3\'-TERMINII_OF_NASCENT_RNA_POL_III_TRANSCRIPTS_BY_LA_AUTOANTIGEN_'_(PDB_00867)
632 +UGCUGUUUUUGCUGUUUU
633 +.((.((....)).))...
634 +>>__'RO_AUTOANTIGEN_COMPLEXED_WITH_RNAS_'_(PDB_00868)
635 +GCUGGUCCGAUUGACUAGCCGCUGGUCCGAUUGACUAGCCUCCGAGGUCCGA
636 +(((((((.....))))))).(((((((.....))))))).............
637 +>>__'HIV-1_DIS_RNA_SUBTYPE_F-_ZN_SOAKED_'_(PDB_00869)
638 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
639 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
640 +>>__'3\'-END_SPECIFIC_RECOGNITION_OF_HISTONE_MRNA_STEM-LOOP_BY_3\'-_EXONUCLEASE_'_(PDB_00883)
641 +GGCUCUUUUCAGAGCCGGCUCUUUUCAGAGCCAAAA
642 +((((((....))))))((((((....))))))....
643 +>>__'SOLUTION_STRUCTURE_OF_BIV_TAR_HAIRPIN_COMPLEXED_TO_JDV_TAT_ARGININE-RICH_MOTIF_'_(PDB_00884)
644 +GGCUCGUGUAGCUCAUUAGCUCCGAGCC
645 +.(((((...((((....)))).))))).
646 +>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MONOCLINIC_FORM_'_(PDB_00886)
647 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
648 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
649 +>>__'MS2_COAT_PROTEIN/RNA_COMPLEX_'_(PDB_00887)
650 +UGAGGAUCACCCAUGAGGAUCACCCA
651 +((.((....))))((.((....))))
652 +>>__'RNA_BACTERIOPHAGE_MS2_COAT_PROTEIN/RNA_COMPLEX_'_(PDB_00888)
653 +AUGAGGAUUACCCAUGUGAGGAUUACCCA
654 +(((.((....))))).((.((....))))
655 +>>__'STRUCTURE_OF_BACTERIOPHAGE_COAT_PROTEIN-LOOP_RNA_COMPLEX_'_(PDB_00889)
656 +GGAUCACCGGAUCACC
657 +((....))((....))
658 +>>__'STRUCTURE_OF_BACTERIOPHAGE_COAT_PROTEIN-LOOP_RNA_COMPLEX_'_(PDB_00890)
659 +ACAUGAGGAUCACCCAUGUACAUGAGGAUCACCCAUGU
660 +(((((.((....)))))))(((((.((....)))))))
661 +>>__'CONFORMATIONAL_CHANGE_OF_PSEUDOURIDINE_55_SYNTHASE_UPON_ITS_ASSOCIATION_WITH_RNA_SUBSTRATE_'_(PDB_00891)
662 +GGCCACGGUUCGAAUCCGUGGCGGCCACGGUUCGAAUCCGUGGC
663 +((((((((.......))))))))(((((((.......)))))))
664 +>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_UUUOH_3\'-TERMINII_OF_NASCENT_RNA_POL_III_TRANSCRIPTS_BY_LA_AUTOANTIGEN_'_(PDB_00896)
665 +UGCUGUUUUUGCUGUUUU
666 +.((.((....)).))...
667 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_TO_GLUTAMINE_AND_2\'DEOXY_A76_GLUTAMINE_TRNA_'_(PDB_00901)
668 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
669 +((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
670 +>>__'COUPLING_OF_ACTIVE_SITE_MOTIONS_AND_RNA_BINDING_'_(PDB_00902)
671 +GGCAACGGUUCGAUCCCGUUGC
672 +.(((((((.......)))))))
673 +>>__'IF2,_IF1,_AND_TRNA_FITTED_TO_CRYO-EM_DATA_OF_E._COLI_70S_INITIATION_COMPLEX_'_(PDB_00903)
674 +GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
675 +(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
676 +>>__'RNA_STEMLOOP_FROM_BACTERIOPHAGE_QBETA_COMPLEXED_WITH_AN_N87S_MUTANT_MS2_CAPSID_'_(PDB_00905)
677 +UGUCUAAGACAG
678 +((((...)))).
679 +>>__'CRYSTAL_STRUCTURE_OF_A_LUTEOVIRAL_RNA_PSEUDOKNOT_AND_MODEL_FOR_A_MINIMAL_RIBOSOMAL_FRAMESHIFTING_MOTIF_'_(PDB_00918)
680 +GCGGCACCGUCCGCUCAAACAAACGG
681 +((((..[[[.)))).........]]]
682 +>>__'TAR_RNA_RECOGNITION_BY_A_CYCLIC_PEPTIDOMIMETIC_OF_TAT_PROTEIN_'_(PDB_00921)
683 +GGCUCGUGUAGCUCAUUAGCUCCGAGCC
684 +((((((...((((....)))).))))))
685 +>>__'DISSECTING_THE_ROLES_OF_A_STRICTLY_CONSERVED_TYROSINE_IN_SUBSTRATE_RECOGNITION_AND_CATALYSIS_BY_PSEUDOURIDINE_55_SYNTHASE_'_(PDB_00923)
686 +CCACGGUUCGAAUCCGUGGC
687 +((((((.......)))))).
688 +>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_00926)
689 +GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCA
690 +((.((((..(((((.....)))))...((((.....)))).......(((((.......))))))))).)).
691 +>>__'CRYSTAL_STRUCTURE_(I)_OF_NOVA-1_KH1/KH2_DOMAIN_TANDEM_WITH_25_NT_RNA_HAIRPIN_'_(PDB_00927)
692 +CGCGGAUCAGUCACCCAAGCGCG
693 +((((((.........))))))..
694 +>>__'CRYSTAL_STRUCTURE_(II)_OF_NOVA-1_KH1/KH2_DOMAIN_TANDEM_WITH_25NT_RNA_HAIRPIN_'_(PDB_00928)
695 +CUCGCGGAUCAGUCACCCAAGCGAG
696 +((((((((.........))))))))
697 +>>__'SOLUTION_STRUCTURE_OF_THE_C27A_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_20_LOWEST_ENERGY_STRUCTURES_'_(PDB_00930)
698 +AGUGGCGCCGACCACUUAAAAACAACGG
699 +(((((..[[[.))))).........]]]
700 +>>__'SOLUTION_STRUCTURE_OF_THE_C27A_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_AVERAGE_STRUCTURE_'_(PDB_00931)
701 +AGUGGCGCCGACCACUUAAAAACAACGG
702 +(((((..[[[.))))).........]]]
703 +>>__'RNA_STEMLOOP_OPERATOR_FROM_BACTERIOPHAGE_QBETA_COMPLEXED_WITH_AN_N87S,E89K_MUTANT_MS2_CAPSID_'_(PDB_00940)
704 +GUCUAAGACAAG
705 +(((...)))...
706 +>>__'RNA_STEMLOOP_FROM_BACTERIOPHAGE_MS2_COMPLEXED_WITH_AN_N87S,_E89K_MUTANT_MS2_CAPSID_'_(PDB_00941)
707 +AUGAGGAUUACCCAUGUGAGGAUUACCCAU
708 +(((.((....))))).((.((....)))).
709 +>>__'MS2_WILD-TYPE_RNA_STEMLOOP_COMPLEXED_WITH_AN_N87S_MUTANT_MS2_CAPSID_'_(PDB_00942)
710 +AUGAGGAUUACCCAUGAUGAGGAUUACCCAU
711 +(((.((....))))).(((.((....)))))
712 +>>__'CRYSTAL_STRUCTURE_OF_STAPHYLOCOCCUS_AUREUS_TRNA_ADENOSINE_DEAMINASE,_TADA,_IN_COMPLEX_WITH_RNA_'_(PDB_00943)
713 +UUGACUACGGAUCAAUUGACUACGGAUCAAGACUACGGUUUGACUACGGAUCAA
714 +(((((.....)))))(((((.....))))).........(((((.....)))))
715 +>>__'GUANINE_RIBOSWITCH_C74U_MUTANT_BOUND_TO_2,6-DIAMINOPURINE_'_(PDB_00944)
716 +GACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC
717 +((((((.....(((((.[[[.[[)))))..........((((((]]..]]]))))))..))))))
718 +>>__'COMPLETE_RNA_POLYMERASE_II-RNA_INHIBITOR_COMPLEX_'_(PDB_00945)
719 +CAGCACUGAUUGCGGUCGAGGUAGCUUGAUG
720 +.((((.....))))((((((....)))))).
721 +>>__'RNA_RECOGNITION_BY_THE_VTS1_SAM_DOMAIN_'_(PDB_00948)
722 +GGAGGCUCUGGCAGCUUUC
723 +(((((((.....)))))))
724 +>>__'STRUCTURE_OF_THE_SMAUG_RECOGNITION_RNA_ELEMENT_'_(PDB_00949)
725 +GGAGGCUCUGGCAGCUUUC
726 +(((((((.....)))))))
727 +>>__'STRUCTURE_OF_HIV-1(LAI)_GENOMIC_RNA_DIS_'_(PDB_00950)
728 +CUUGCUGAAGCGCGCACGGCAAGCUUGCUGAAGCGCGCACGGCAAG
729 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
730 +>>__'STRUCTURE_OF_HIV-1(MAL)_GENOMIC_RNA_DIS_'_(PDB_00951)
731 +CUUGCUGAGGUGCACACAGCAAGCUUGCUGAGGUGCACACAGCAAG
732 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
733 +>>__'CRYSTAL_STRUCTURE_OF_E._COLI_5-METHYLURIDINE_METHYLTRANSFERASE_RUMA_IN_COMPLEX_WITH_RIBOSOMAL_RNA_SUBSTRATE_AND_S-ADENOSYLHOMOCYSTEINE._'_(PDB_00961)
734 +AGCGAAAUUCCUUGUCGGGUAAGUUCCGACAGCGAAAUUCCUUGUCGGGUAAGUUCCGAC
735 +.............(((((.......))))).............(((((.......)))))
736 +>>__'MS2_(N87A_MUTANT)-_RNA_HAIRPIN_COMPLEX_'_(PDB_00963)
737 +AUGAGGAUUACCCAUUGAGGAUUACCCA
738 +(((.((....)))))((.((....))))
739 +>>__'MS2_(N87AE89K_MUTANT)-_RNA_HAIRPIN_COMPLEX_'_(PDB_00964)
740 +ACAUGAGGAUUACCCAUGUCAUGAGGAUUACCCAUG
741 +(((((.((....)))))))..((.........))..
742 +>>__'MS2_(N87AE89K_MUTANT)-_VARIANT_QBETA_RNA_HAIRPIN_COMPLEX_'_(PDB_00965)
743 +UGUCUAAGACUGGUCUAAGAC
744 +.(((...)))..(((...)))
745 +>>__'MS2_(N87AE89K_MUTANT)-_QBETA_RNA_HAIRPIN_COMPLEX_'_(PDB_00966)
746 +UGUCUAAGACAGUGUCUAAGACA
747 +.(((...)))..((((...))))
748 +>>__'MS2-RNA_HAIRPIN_(5BRU-5)_COMPLEX_'_(PDB_00968)
749 +CAUGAGGAUUACCCAUGCAUGAGGAUUACCCAUG
750 +((((.((....))))))((((.((....))))))
751 +>>__'MS2-RNA_HAIRPIN_(2ONE-5)_COMPLEX_VIRUS_'_(PDB_00970)
752 +CAUGAGGAUUACCCAUGCAUGAGGAUUACCCAUG
753 +((((.((....))))))..((.((....))))..
754 +>>__'MS2-RNA_HAIRPIN_(2THIOURACIL-5)_COMPLEX_'_(PDB_00971)
755 +CAUGAGGAUUACCCAUGUGAGGAUUACCCA
756 +((((.((....))))))((.((....))))
757 +>>__'MS2-RNA_HAIRPIN_(2SU-5-6)_COMPLEX_'_(PDB_00972)
758 +CAUGAGGAUUACCCAUGUGAGGAUUACCCA
759 +((((.........))))((.........))
760 +>>__'MS2-RNA_HAIRPIN_(A-5)_COMPLEX_'_(PDB_00973)
761 +AUGAGGAUAACCCAUGAGGAUAACCCA
762 +.((.((....))))((.((....))))
763 +>>__'MS2-RNA_HAIRPIN_(G-5)_COMPLEX_'_(PDB_00974)
764 +AUGAGGAUGACCCAUUGAGGAUGACCCA
765 +(((.((....)))))((.((....))))
766 +>>__'REFINEMENT_OF_P4_STEMLOOP_STRUCTURE_USING_RESIDUAL_DIPOLAR_COUPLING_DATA_'_(PDB_00975)
767 +GGAAGUCCGGUCUUCGGACCGGCUUCC
768 +.((((.(((((......))))))))).
769 +>>__'REFINEMENT_OF_RNASE_P_P4_STEMLOOP_STRUCTURE_USING_RESIDUAL_DIPOLAR_COUPLINGS-_COBALT(III)_HEXAMMINE_COMPLEX_STRUCTURE_'_(PDB_00977)
770 +GGAAGUCCGGUCUUCGGACCGGCUUCC
771 +(((((.(((((......))))))))))
772 +>>__'SOLUTION_RNA_STRUCTURE_OF_LOOP_REGION_OF_THE_HIV-1_DIMERIZATION_INITIATION_SITE_IN_THE_KISSING-LOOP_DIMER_'_(PDB_00988)
773 +GCUGAAGUGCACACGGCGCUGAAGUGCACACGGC
774 +((((..[[[[[[.))))((((..]]]]]].))))
775 +>>__'SOLUTION_RNA_STRUCTURE_MODEL_OF_THE_HIV-1_DIMERIZATION_INITIATION_SITE_IN_THE_KISSING-LOOP_DIMER_'_(PDB_00990)
776 +GGGUCGGCUUGCUGAAGUGCACACGGCAAGAGGCGACCCGGGUCGGCUUGCUGAAGUGCACACGGCAAGAGGCGACCC
777 +(((((((((((((((.[[[[[[)))))))))..))))))((((((((((((((..]]]]]].))))))))..))))))
778 +>>__'COCRYSTAL_STRUCTURE_OF_AN_RNA_SULFURATION_ENZYME_MNMA_AND_TRNA-GLU_IN_THE_PRE-REACTION_STATE_'_(PDB_00999)
779 +GUCCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG
780 +..((.....(((((.......)))))(((((((.....)))))))....((((.......))))...)).
781 +>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_01002)
782 +GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCACCA
783 +(((((((....(((.....)))...((((((.....)))))).....(((((.......))))))))))))....
784 +>>__'COMPLEX_STRUCTURE_OF_CCA_ADDING_ENZYME_WITH_MINI-HELIX_LACKING_CCA_'_(PDB_01003)
785 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCA
786 +(((((((..(((.......)))..))))))).
787 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDC_'_(PDB_01004)
788 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAC
789 +((((((((((((.......))))))))))))..
790 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDC_AND_CTP_'_(PDB_01005)
791 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAC
792 +((((((((((((.......))))))))))))..
793 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDCC_'_(PDB_01006)
794 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
795 +((((((((((((.......))))))))))))...
796 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDCC_AND_ATP_'_(PDB_01007)
797 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
798 +((((((((((((.......))))))))))))...
799 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINICCA_'_(PDB_01008)
800 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACCA
801 +((((((((((((.......))))))))))))....
802 +>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_AND_O-PHOSPHOSERINE_'_(PDB_01009)
803 +GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
804 +((((((([[(((]].......)))..((((.......))))......(((((.......))))))))))))
805 +>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_'_(PDB_01010)
806 +GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
807 +..((((([[(((]].......)))..(((((.....)))))......(((((.......))))))))))..
808 +>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAOPAL_AND_O-PHOSPHOSERINE_("OPAL_COMPLEX")_'_(PDB_01011)
809 +GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUUCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
810 +(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
811 +>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAAMBER_AND_O-PHOSPHOSERINE_("AMBER_COMPLEX")_'_(PDB_01012)
812 +GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUCUAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
813 +(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
814 +>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME,_MINI-DCC_AND_CTP_'_(PDB_01013)
815 +GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
816 +((((((((((((.......))))))))))))...
817 +>>__'GUANINE_RIBOSWITCH_A21U,_U75A_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01020)
818 +GGACAUUUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACAAUGUCCA
819 +.((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))..
820 +>>__'GUANINE_RIBOSWITCH_A21G,_U75C_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01021)
821 +GGACAUGUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACCAUGUCCA
822 +.((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))..
823 +>>__'GUANINE_RIBOSWITCH_U22A,_A52U_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01022)
824 +GGACAUAAAAUCGCGUGGAUAUGGCACGCAAGUUUCUUCCGGGCACCGUAAAUGUCCGACUAUGUCCA
825 +(((((((.....(((((.[[..[[)))))..........((((((]]...]]))))))..))))))).
826 +>>__'GUANINE_RIBOSWITCH_U22C,_A52G_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01023)
827 +GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCA
828 +(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))).
829 +>>__'GUANINE_RIBOSWITCH_U47C_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01024)
830 +GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGCUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCCA
831 +(((((((.....(((((.[[..[[)))))..........((((((]]...]]))))))..))))))).
832 +>>__'STRUCTURE_OF_THE_SRE_RNA_'_(PDB_01025)
833 +GGAGAGGCUCUGGCAGCUUUUCC
834 +(((((((((.....)))))))))
835 +>>__'STRUCTURE_OF_THE_SAM_DOMAIN_OF_VTS1P_IN_COMPLEX_WITH_RNA_'_(PDB_01026)
836 +GGAGAGGCUCUGGCAGCUUUUCC
837 +(((((((((.....)))))))))
838 +>>__'NMR_SOLUTION_OF_HIV-1_LAI_KISSING_COMPLEX_'_(PDB_01040)
839 +GGUUGCUGAAGCGCGCACGGCAACGGUUGCUGAAGCGCGCACGGCAAC
840 +.(((((((..[[[[[[.))))))).(((((((..]]]]]].)))))))
841 +>>__'SOLUTION_NMR_STRUCTURE_OF_DOMAIN_5_FROM_THE_PYAIELLA_LITTORALIS_(PL)_GROUP_II_INTRON_'_(PDB_01042)
842 +GAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUC
843 +((((((((.(((((....)))))...))))))))
844 +>>__'CRYSTAL_STRUCTURE_OF_AA-AGO_WITH_EXTERNALLY-BOUND_SIRNA_'_(PDB_01044)
845 +AGACAGCAUAUAUGCUGUCUUUAGACAGCAUAUAUGCUGUCUUU
846 +.((((((((((.((((((......)))))).))))))))))...
847 +>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_NEAMINE_'_(PDB_01046)
848 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
849 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
850 +>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_NEOMYCIN_'_(PDB_01047)
851 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
852 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
853 +>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_RIBOSTAMYCIN_'_(PDB_01048)
854 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
855 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
856 +>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_LIVIDOMYCIN_'_(PDB_01049)
857 +CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
858 +(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
859 +>>__'SOLUTION_STRUCTURE_OF_A_CONSERVED_RNA_HAIRPIN_OF_EEL_LINE_UNAL2_'_(PDB_01050)
860 +GGUUGUACGUCGCUUUGGAUAAAAGCGUCUGCGACC
861 +((((((..(((((((.......))))))).))))))
862 +>>__'THE_STRUCTURE_OF_STEM_LOOP_IV_OF_TETRAHYMENA_TELOMERASE_RNA_'_(PDB_01051)
863 +GAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUC
864 +(((((......(((..(((((.....))))).)))...)))))
865 +>>__'CRYSTAL_STRUCTURE_OF_RNASE_Z/TRNA(THR)_COMPLEX_'_(PDB_01053)
866 +GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU
867 +(((((((..((((........))))...(((((.......)))))))))))).
868 +>>__'SOLUTION_STRUCTURE_OF_THE_HELIX_II_TEMPLATE_BOUNDARY_ELEMENT_FROM_TETRAHYMENA_TELOMERASE_RNA_'_(PDB_01056)
869 +GGCAGAUCUGUAAUAGAACUGCC
870 +(((((((((.....)))))))))
871 +>>__'A_DUAL_MODE_OF_RNA_RECOGNITION_BY_THE_RBMY_PROTEIN_'_(PDB_01057)
872 +GGACUGUCCACAAGACAGUCC
873 +((((((((.....))))))))
874 +>>__'SOLUTION_STRUCTURE_OF_THE_ANTICODON_LOOP_OF_S._POMBE_TRNAI_INCLUDING_THE_NATURALLY_OCCURRING_N6-THREONYL_ADENINE_'_(PDB_01058)
875 +ACGGGCUCAUAACCCGU
876 +(((((((...)))))))
877 +>>__'NMR_STRUCTURE_OF_THE_AQUIFEX_AEOLICUS_TMRNA_PSEUDOKNOT_PK1_'_(PDB_01059)
878 +GGGGUGGCUCCCCUAACAGCCG
879 +((((.[[[.)))).....]]].
880 +>>__'MODIFIED_PYRIMIDINES_SPECIFICALLY_BIND_THE_PURINE_RIBOSWITCH_'_(PDB_01066)
881 +GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU
882 +(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))).
883 +>>__'RNA_RECOGNITION_AND_CLEAVAGE_BY_AN_SPLICING_ENDONUCLEASE_'_(PDB_01074)
884 +GCGACCGACCAUAGCUGCUGCAGCGGUCAAAGGUCGCGCGACCGACCAUAGCUGCAUGCAGCGGUCAAAGGUCGC
885 +.(((((((((...((((...))))))))...))))).((((((((((...((........))))))...))))))
886 +>>__'TRANSLOCATION_OF_A_TRNA_WITH_AN_EXTENDED_ANTICODON_THROUGH_THE_RIBOSOME_'_(PDB_01084)
887 +GGCCAGACUCCCGAAUCUGGCC
888 +(((((((........)))))))
889 +>>__'SOLUTION_STRUCTURE_OF_A_PURINE_RICH_HEXALOOP_HAIRPIN_BELONGING_TO_PGY/MDR1_MRNA_AND_TARGETED_BY_ANTISENSE_OLIGONUCLEOTIDES_'_(PDB_01086)
890 +GAGGUCGGGAUGGAUCUC
891 +((((((......))))))
892 +>>__'SOLUTION_STRUCTURE_OF_THE_TETRAHYMENA_TELOMERASE_RNA_STEM_IV_TERMINAL_LOOP_'_(PDB_01097)
893 +GGCGAUACACUAUUUAUCGCC
894 +((((((((.....))))))))
895 +>>__'STRUCTURE_OF_THE_AAGU_TETRALOOP_'_(PDB_01108)
896 +GGCGUGAUCAAGUGAUCGCGCC
897 +(((((((((....)))))))))
898 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_MANGANESE_IONS_'_(PDB_01111)
899 +GCGACUCGGGGUGCCCUCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
900 +((((((((((((((((......))))......)))))).(((((((.((((......))))))))))))))))).
901 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_CALCIUM_IONS_'_(PDB_01112)
902 +GCGACUCGGGGUGCCCUGCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUCCAGCGAGGGAAGUCGCA
903 +((((((((((((((((.......))))......)))))).(((((((.((((.....))))))))))))))))).
904 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_BARIUM_IONS_'_(PDB_01113)
905 +GCGACUCGGGGUGCCCUCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
906 +((((((((((((((((......))))......)))))).(((((((.((((......))))))))))))))))).
907 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_MONOPHOSPHATE_'_(PDB_01114)
908 +GCGACUCGGGGUGCCCUGCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
909 +((((((((((((((((.......))))......)))))).(((((((.((((......))))))))))))))))).
910 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_BENFOTIAMINE_'_(PDB_01115)
911 +GCGACUCGGGGUGCCCUGCAAGGCUGAGAAAACCCGUAUACCUGACUGGAUAAUGCCAGCGUAGGGAAGUCGCA
912 +((((((((((((((((....))))......))))))...((((((((((......)))))).)))).)))))).
913 +>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_PYRITHIAMINE_'_(PDB_01116)
914 +GCGACUCGGGGUGCCCGCGUAAGGCUGAGAAAACCCGUAACCUGAUGGAUAAUCCAGAGGGAAGUCGCA
915 +((((((((((((((((.....))))......)))))).(((((..............))))))))))).
916 +>>__'CRYSTAL_STRUCTURE_OF_AN_H/ACA_BOX_RNP_FROM_PYROCOCCUS_FURIOSUS_'_(PDB_01118)
917 +GGGUCCGCCUUGAUGCCCGGGUGAAAGCAUGAUCCCGGGUAAUAUGGCGGACCCACA
918 +(((((((((.....((((((((((......)))))))))).....)))))))))...
919 +>>__'CRYSTAL_STRUCTURE_OF_PSEUDOURIDINE_SYNTHASE_RLUA:_INDIRECT_SEQUENCE_READOUT_THROUGH_PROTEIN-INDUCED_RNA_STRUCTURE_'_(PDB_01126)
920 +GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC
921 +(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))
922 +>>__'CRYSTAL_STRUCTURE_OF_IRON_REGULATORY_PROTEIN_1_IN_COMPLEX_WITH_FERRITIN_H_IRE-RNA_'_(PDB_01130)
923 +GUUCUUGCUUCAACAGUGUUUGAACGGAACGUUCUUGCUUCAACAGUGUUUGAACGGAAC
924 +(((((...(((((......))))).)))))(((((...(((((......))))).)))))
925 +>>__'SOLUTION_STRUCTURE_OF_THE_APICAL_STEM-LOOP_OF_THE_HUMAN_HEPATITIS_B_VIRUS_ENCAPSIDATION_SIGNAL_'_(PDB_01133)
926 +GGCCUCCAAGCUGUGCCUUGGGUGGCC
927 +((((((((((......)))))).))))
928 +>>__'PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_TRNA_AND_A_PHENYLALANYL-ADENYLATE_ANALOG_'_(PDB_01134)
929 +GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
930 +(((((((....((........))...((((((.....)))))).....((((.........)))))))))))....
931 +>>__'MS2-RNA_HAIRPIN_(C-7)_COMPLEX_'_(PDB_01135)
932 +AUGAGGCUCACCCAUGUGAGGCUCACCCA
933 +(((.((....))))).((.((....))))
934 +>>__'MS2-RNA_HAIRPIN_(4ONE-5)_COMPLEX_'_(PDB_01136)
935 +AUGAGGAUUACCCAUAUGAGGAUUACCCAU
936 +.((.((....))))..((.((....)))).
937 +>>__'MS2-RNA_HAIRPIN_(C-10)_COMPLEX_'_(PDB_01137)
938 +UGCGGAUCACCCAUGCGGAUCACCCA
939 +((.((....))))((.((....))))
940 +>>__'MS2-RNA_HAIRPIN_(G-10)_COMPLEX_'_(PDB_01138)
941 +AUCGCGAUUACGGAUCGCGAUUACGG
942 +(((.((....)))))..((....)).
943 +>>__'STRUCTURAL_BASIS_OF_RSMA/CSRA_RNA_RECOGNITION:_STRUCTURE_OF_RSME_BOUND_TO_THE_SHINE-DALGARNO_SEQUENCE_OF_HCNA_MRNA_'_(PDB_01145)
944 +GGGCUUCACGGAUGAAGCCCGGGCUUCACGGAUGAAGCCC
945 +(((((((......)))))))(((((((......)))))))
946 +>>__'MODEL_FOR_THIOSTREPTON_BINDING_TO_THE_RIBOSOMAL_L11-RNA_'_(PDB_01146)
947 +GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
948 +((((((.((..(((.........)))..)).........(((......))).))))))
949 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E.COLI_TRNA-VAL3_WITH_NO_MODIFICATIONS_'_(PDB_01147)
950 +CCUCCCUUACAAGGAGG
951 +((((((.....))))))
952 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E._COLI_TRNA-_VAL3_WITH_2_MODIFICATIONS_(CMO5U34_M6A37)_'_(PDB_01148)
953 +CCUCCCUUACAAGGAGG
954 +(((((.......)))))
955 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E._COLI_TRNA-_VAL3_WITH_1_MODIFICATION_(CMO5U34)_'_(PDB_01149)
956 +CCUCCCUUACAAGGAGG
957 +((((((.....))))))
958 +>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E.COLI_TRNA-VAL3_WITH_1_MODIFICATION_(M6A37)_'_(PDB_01151)
959 +CCUCCCUUACAAGGAGG
960 +((((((.....))))))
961 +>>__'SOLUTION_STRUCTURE_OF_THE_FRAMESHIFT-INDUCING_RNA_STEM-LOOP_IN_SIV_'_(PDB_01152)
962 +GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC
963 +((((((((((((..((...)).))))))))))))
964 +>>__'CRYSTAL_STRUCTURE_OF_RNASE_III_FROM_AQUIFEX_AEOLICUS_COMPLEXED_WITH_DS-RNA_AT_1.7-ANGSTROM_RESOLUTION_'_(PDB_01165)
965 +AAGGUCAUUCGAGUGGCCUUGCAAGGUCAUUCGAGUGGCCUUGC
966 +((((((((([[)))))))))..(((((((((]])))))))))..
967 +>>__'SOLUTION_STRUCTURE_OF_U2_SNRNA_STEM_I_FROM_S._CEREVISIAE_'_(PDB_01168)
968 +GGUUUGCCUUUUGGCUUACC
969 +((((((((....))))))))
970 +>>__'HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR_WITH_C75U_MUTATION_AND_BOUND_TO_MONOVALENT_CATION_TL+_'_(PDB_01185)
971 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
972 +.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
973 +>>__'HEPATITIS_DELTA_VIRUS_RIBOZYME_PRECURSOR_STRUCTURE,_WITH_C75U_MUTATION,_BOUND_TO_TL+_AND_COBALT_HEXAMMINE_(CO(NH3)_63+)_'_(PDB_01190)
974 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
975 +..((((((...[[[[[[(((.[[.....))))))))).]]...(((((..........)))))....]]]]]]
976 +>>__'NMR_STRUCTURE_OF_A_KISSING_COMPLEX_FORMED_BETWEEN_THE_TAR_RNA_ELEMENT_OF_HIV-1_AND_A_LNA/RNA_APTAMER_'_(PDB_01194)
977 +GGAGCCUGGGAGCUCCCACGGUCCCAGACGUG
978 +((((([[[[[.)))))(((((.]]]]])))))
979 +>>__'STRUCTURE_OF_A_HUMAN_PRP31-15.5K-U4_SNRNA_COMPLEX_'_(PDB_01199)
980 +AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU
981 +(((((.(((...((((.....))))))))))))(((((.(((...((((.....))))))))))))
982 +>>__'SOLUTION_STRUCTURE_OF_AN_RRNA_SUBSTRATE_BOUND_TO_THE_PSEUDOURIDYLATION_POCKET_OF_A_BOX_H/ACA_SNORNA_'_(PDB_01202)
983 +GGACCCGCCACUGCAGAGAUGCAAUCCAGUGGUCC
984 +(((((......((((....)))).......)))))
985 +>>__'STRUCTURE_OF_THE_MRNA_BINDING_FRAGMENT_OF_ELONGATION_FACTOR_SELB_IN_COMPLEX_WITH_SECIS_RNA._'_(PDB_01205)
986 +GGCGUUGCCGGUCUGGCAACGCCGGCGUUGCCGGUCUGGCAACGCC
987 +(((((((((.....)))))))))(((((((((.....)))))))))
988 +>>__'NMR_STRUCTURE_OF_A_KISSING_COMPLEX_FORMED_BETWEEN_THE_TAR_RNA_ELEMENT_OF_HIV-1_AND_A_LNA_MODIFIED_APTAMER_'_(PDB_01206)
989 +GGAGCCUGGGAGCUCCCACGGUCCCAGACGUG
990 +((((([[[[[[)))))(((((]]]]]])))))
991 +>>__'SOLUTION_STRUCTURE_OF_THE_CR7_TERMINAL_HAIRPIN_LOOP_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_01237)
992 +GGAGUGCCUGAGCUGUGGCACUCC
993 +((((((((........))))))))
994 +>>__'SOLUTION_STRUCTURE_OF_THE_U64_H/ACA_SNORNA_3\'_TERMINAL_HAIRPIN_LOOP_'_(PDB_01238)
995 +GGAGUGCCUUACUGUGGCACUCC
996 +((((((((.......))))))))
997 +>>__'SOLUTION_STRUCTURE_OF_THE_U85_C/D-H/ACA_SCARNA_5\'_TERMINAL_HAIRPIN_LOOP_'_(PDB_01239)
998 +GGCACAGAGUUAUGUGCC
999 +(((((((....)))))))
1000 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE_'_(PDB_01258)
1001 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
1002 +((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
1003 +>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE_'_(PDB_01259)
1004 +GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
1005 +((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
1006 +>>__'SOLUTION_STRUCTURE_OF_THE_TOBRAMYCIN-RNA_APTAMER_COMPLEX,_NMR,_13_STRUCTURES_'_(PDB_01262)
1007 +ACUUGGUUUAGGUAAUGAGU
1008 +((((((((....))))))))
1009 +>>__'C-TERMINAL_DOMAIN(WH2-WH4)_OF_ELONGATION_FACTOR_SELB_IN_COMPLEX_WITH_SECIS_RNA_'_(PDB_01270)
1010 +GGCGUUGCCGGUCUGGCAACGCCGGCGUUGCCGGUCUGGCAACGCC
1011 +(((((((((.....)))))))))(((((((((.....)))))))))
1012 +>>__'CRYSTAL_STRUCTURE_OF_AN_ESCHERICHIA_COLI_TRNAGLY_MICROHELIX_AT_2.0_ANGSTROM_RESOLUTION_'_(PDB_01281)
1013 +GCGGGAAGCGGGAAUUCCCGCUUCCCGC
1014 +((((((([[[[[[[)))))))]]]]]]]
1015 +>>__'CRYSTAL_STRUCTURE_OF_DOMAIN_III_OF_THE_CRICKET_PARALYSIS_VIRUS_IRES_RNA_'_(PDB_01299)
1016 +GGUUAUUCAGAUUAGGUAGUCGAAUGACCUAAGAAAUUUACCU
1017 +((((((((.((..[[[[[.)))))))))).........]]]]]
1018 +>>__'5\'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3\'_'_(PDB_01313)
1019 +GAUCACUUCGGUGAUCACUUCGGU
1020 +....((((((((....))))))))
1021 +>>__'SOLUTION_STRUCTURE_OF_HIV-1_REV_PEPTIDE-RNA_APTAMER_COMPLEX_'_(PDB_01332)
1022 +GGUGUCUUGGAGUGCUGAUCGGACACC
1023 +(((((((..((.......)))))))))
1024 +>>__'MS2_PROTEIN_CAPSID/RNA_COMPLEX_'_(PDB_01337)
1025 +CCGGAGGAUCACCACGGGCGGAGGAUCACCACGG
1026 +((((.((....)))))).(((.((....))))).
1027 +>>__'F6_APTAMER_MS2_COAT_PROTEIN_COMPLEX_'_(PDB_01338)
1028 +CCACAGUCACUGGGCAGUCACUGG
1029 +((.(((...)))))(((...))).
1030 +>>__'MS2_PROTEIN_CAPSID/RNA_COMPLEX_'_(PDB_01340)
1031 +UCGCCAACAGGCGGGCCAACAGGCG
1032 +(((((....)))))(((....))).
1033 +>>_PKB1:_Bovine_Leukemia_Virus_(BLV)
1034 +AAAAAACUAAUAGAGGGGGGACUUAGCGCCCCCCAAACCGUAACCCC
1035 +..............[[[[[[.....(((]]]]]]....)))......
1036 +>>_PKB2:_Beet_Western-Yellows_Virus_(BWYV)
1037 +GGGAAACGGAGUGCGCGGCACCGUCCGCGGAACAAACGGAGAAGGCAGCU
1038 +.............[[[[[..((((]]]]]......))))...........
1039 +>>_PKB3:_Equine_Infectious_Anemic_Virus_(EIAV)
1040 +AAAAAACGGGAAGCAAGGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCCGAU
1041 +................[[[[[[...((((]]]]]]............))))...
1042 +>>_PKB4:_Feline_Immunodeficiency_Virus_(FIV)
1043 +GGGAAACUGGAAGGCGGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC
1044 +...............[[[[[..((((((]]]]]...........))))))
1045 +>>_PKB5:_turnip_yellow_mosaic_virus_(TYMV)
1046 +CGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACC
1047 +...............(((....[[[[[)))...]]]]]...
1048 +>>_PKB6:_kennedya_yellow_mosaic_virus_(KYMV-BP)
1049 +GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
1050 +...............(((...[[[[[[)))...]]]]]]...
1051 +>>_PKB7:_cacao_yellow_mosaic_virus_(CaYMV)
1052 +GGUGGUGCAACUCCCCCGUCCUCCCGAACGUCAUCGGGACCA
1053 +................(((..[[[[[[)))...]]]]]]...
1054 +>>_PKB8:_physalis_mottle_virus_(PhyMV)
1055 +UGGGUGCAACUCCCCCCCCUUCCGUGGGUAACGGAAACCA
1056 +..............(((..[[[[[[)))..]]]]]]....
1057 +>>_PKB9:_desmodium_yellow_mottle_virus_(DYMV)
1058 +GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
1059 +...............(((...[[[[[[)))...]]]]]]...
1060 +>>_PKB10:_ononis_yellow_mosaic_virus_(OYMV)
1061 +UGGGUUCAACUCCCCCCCUUUUCCGAGGGUAUCGGAAACC
1062 +..............(((...[[[[[[)))..]]]]]]...
1063 +>>_PKB11:_clitoria_yellow_vein_virus_(CYVV)
1064 +UGGGUGCAACCCCCCCGUCCAUCUCGAACGUCAUCGAGACCA
1065 +...............(((...[[[[[[)))...]]]]]]...
1066 +>>_PKB12:_wild_cucumber_mosaic_virus_(WCMV)
1067 +CGGGUGCAACCCCCCCUCCCCCCGUAGGUUAACGGGACCA
1068 +..............(((...[[[[[)))...]]]]]....
1069 +>>_PKB13:_calopogonium_yellow_vein_virus_(CaYVV)
1070 +GGGGUGCGACUCCCCCGUCUAUCCUGAACGUCAUCAGGACCA
1071 +...............(((...[[[[[[)))...]]]]]]...
1072 +>>_PKB14:_andean_potato_latent_virus_(APLV)
1073 +CGGGUGCGACUCCCCCCCCUCCUGUGGGCUACAGGAACCA
1074 +..............(((..[[[[[[)))..]]]]]]....
1075 +>>_PKB15:_eggplant_mosaic_virus_(EMV)
1076 +UGGGUGCGACUCCCCCCCCUCCCGUGGGUCAACGGGAACCA
1077 +..............(((..[[[[[[)))...]]]]]]....
1078 +>>_PKB16:_okra_mosaic_virus_(OMV)
1079 +GGGGUGCAACUCCCCCGCCCAUCUCGAGCGUCAUCGAGACCA
1080 +...............(((...[[[[[[)))...]]]]]]...
1081 +>>_PKB17:_tobacco_mosaic_virus_(CcTMV)
1082 +GGGGAGCAUUACCCCCCCAAAACCCUGGGGAUACAGGGCCCA
1083 +...............(((....[[[[[)))...]]]]]....
1084 +>>_PKB18:_tobacco_mosaic_virus_(TMV)
1085 +GGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA
1086 +...............(((...[[[[)))..]]]]....
1087 +>>_PKB19:_pepper_mild_mottle_virus_(PMMV-I)
1088 +GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
1089 +...............(((...[[[[)))..]]]]....
1090 +>>_PKB20:_cucumber_green_mottle_mosaic_virus_(CGMMV)
1091 +GGGGUUCGAAUCCCCCCUUUUCCCCGGGUAGGGGCCCA
1092 +...............(((...[[[[)))..]]]]....
1093 +>>_PKB21:_tobacco_mosaic_virus_(TMV-L)
1094 +GGGAUUCGAAUUCCCCCGGAACCCCCGGUUGGGGCCCA
1095 +...............(((...[[[[)))..]]]]....
1096 +>>_PKB22:_satellite_tobacco_mosaic_virus_(STMV)
1097 +GGGGUUCGAAUCCCUCCCUAACCGCGGGUAAGCGGCCCA
1098 +...............(((...[[[[)))...]]]]....
1099 +>>_PKB23:_tobacco_mild_green_mosaic_virus_(TMGMV)
1100 +GAGGUUCGAAUCCUCCCGUAACCGCCGGUAGCGGCCCA
1101 +...............(((...[[[[)))..]]]]....
1102 +>>_PKB24:_paprika_mild_mottle_virus_(PaMMV)
1103 +GGGGUUCGAAUCCCCCCUUUACCCCGGGUAUGGGGCCCA
1104 +...............(((...[[[[)))...]]]]....
1105 +>>_PKB25:_turnip_vein-clearing_virus_(TVCV)
1106 +GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
1107 +...............(((..[[[[)))..]]]]....
1108 +>>_PKB26:_oilseed_rape_mosaic_virus_(ORMV)
1109 +GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
1110 +...............(((..[[[[)))..]]]]....
1111 +>>_PKB27:_pepper_mild_mottle_virus_(PMMV-S)
1112 +GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
1113 +...............(((...[[[[)))..]]]]....
1114 +>>_PKB28:_odontoglossum_ringspot_virus_(ORSV-S1)
1115 +GGGAUUCGAAUUCCCCCUUACCUCGGGUAGAGGCCCA
1116 +...............(((..[[[[)))..]]]]....
1117 +>>_PKB29:_tobacco_mosaic_virus_(TMVcg)
1118 +GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
1119 +...............(((..[[[[)))..]]]]....
1120 +>>_PKB30:_soil-borne_wheat_mosaic_virus_(SBWMV1)
1121 +GGGGUUCAAAUCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
1122 +...............(((...[[[[[)))...]]]]]....
1123 +>>_PKB31:_soil-borne_wheat_mosaic_virus_(SBWMV2)
1124 +GGGGUUCAAUUCCCCCCCCAUCCGGAGGGUUAUCCGGCCC
1125 +...............(((...[[[[[)))...]]]]]...
1126 +>>_PKB32:_potato_mop-top_virus_(PMTV2)
1127 +GGGUGCAACUCCCCCCCCCUUGGAGGGUAUCCAAGACC
1128 +.............(((..[[[[[[)))..]]]]]]...
1129 +>>_PKB33:_peanut_clump_virus_(PCV1)
1130 +GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
1131 +.............(((....[[[[[)))...]]]]]....
1132 +>>_PKB34:_peanut_clump_virus_(PCV2)
1133 +GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
1134 +.............(((....[[[[[)))...]]]]]....
1135 +>>_PKB35:_Indian_peanut_clump_virus_(IPCV1)
1136 +GGUGCAAAUCCCCCGCCGAUACGGAGCGAUAUCCGUCCCA
1137 +.............(((....[[[[[)))...]]]]]....
1138 +>>_PKB36:_beet_soil-borne_virus_(BSBV1)
1139 +GGGGUGCAAAUCCCCCCCUUUACUUGAGGGAAAUCAAGCCC
1140 +...............(((....[[[[[)))...]]]]]...
1141 +>>_PKB37:_beet_soil-borne_virus_(BSBV2)
1142 +GGGGUGCAAAUCCCCCCCUUAACUUGAGGGAAAUCAAGCCC
1143 +...............(((....[[[[[)))...]]]]]...
1144 +>>_PKB38:_beet_soil-borne_virus_(BSBV3)
1145 +GGGGUGCAACUCCCCCCCUUAACUAGAGGGAAAUCUAGCCC
1146 +...............(((....[[[[[)))...]]]]]...
1147 +>>_PKB39:_beet_virus_Q_(BVQ1)
1148 +GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
1149 +...............(((...[[[[[)))...]]]]]....
1150 +>>_PKB40:_beet_virus_Q_(BVQ2)
1151 +GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCC
1152 +...............(((...[[[[[)))...]]]]]...
1153 +>>_PKB41:_beet_virus_Q_(BVQ3)
1154 +GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
1155 +...............(((...[[[[[)))...]]]]]....
1156 +>>_PKB42:_potato_leafroll_virus_(PLRV-W)
1157 +UUUAAAUGGGCGAGCGGCACCGCCCGCCAAAACAAACGG
1158 +.............((((..[[[.)))).........]]]
1159 +>>_PKB43:_potato_leafroll_virus_(PLRV-S)
1160 +UUUAAAUGGGCAAGCGGCACCGUCCGCCAAAACAAACGG
1161 +.............((((..[[[[))))........]]]]
1162 +>>_PKB44:_cucurbit_aphid-borne_yellows_virus_(CABYV)
1163 +GGGAAACGGGCAGGCGGCGGCGACCGCCGAAACAACCGC
1164 +............(((((..[[[.)))))........]]]
1165 +>>_PKB45:_pea_enation_mosaic_virus_(PEMV)
1166 +GGGAAACGGAUUAUUCCGGUCGACUCCGGAGAAACAAAGUC
1167 +.............((((((..[[[[))))))......]]]]
1168 +>>_PKB46:_barley_yellow_dwarf_virus_(BYDV-NY-RPV)
1169 +GGGAAACGGGAAGGCGGCGGCGUCCGCCGUAACAAACGC
1170 +............(((((..[[[[))))).......]]]]
1171 +>>_PKB47:_Moloney_murine_leukemia_virus_(Mo-MuLV)
1172 +UAGGGAGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGC
1173 +...........((((((((.[[[[[[[)))).))))..................]]]]]]]
1174 +>>_PKB48:_spleen_necrosis_virus_(SNV)
1175 +UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
1176 +...........((((((.(..[[[[[[[).))))))..................]]]]]]]
1177 +>>_PKB49:_E.coli_(Ec_PK1)
1178 +CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC
1179 +(((((.[[[[[[..))))).....]]]]]]
1180 +>>_PKB50:_E.coli_(Ec_PK2)
1181 +CCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAG
1182 +(((((((((((..(((...[[[[[)))..))))....)))))))..........]]]]]
1183 +>>_PKB51:_E.coli_(Ec_PK3)
1184 +GCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGC
1185 +((((...(((((.[[[[[)))))...))))...........]]]]]
1186 +>>_PKB52:_E.coli_(Ec_PK4)
1187 +GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC
1188 +((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]]
1189 +>>_PKB53:_tobacco_mosaic_virus_(TMV_UPD-PK1)
1190 +ACGGAUUGUGUCCGUAAUCACA
1191 +..(((.[[[[))).....]]]]
1192 +>>_PKB54:_tobacco_mosaic_virus_(TMV_UPD-PK2)
1193 +CGUGGUGCGUACGAUAACGCAU
1194 +(((.[[[[[[)))...]]]]]]
1195 +>>_PKB55:_tobacco_mosaic_virus_(TMV_UPD-PK3)
1196 +AGUGUUUUUCCCUCCACUUAAAUCGAAGGG
1197 +((((.....[[[[[))))......].]]]]
1198 +>>_PKB56:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK1)
1199 +UAACGUUGAUAGUGUUGAACUAUC
1200 +((((((.[[[[))))))...]]]]
1201 +>>_PKB57:_tobacco_mosaic_virus_(TMV_PKbulge)
1202 +UGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGA
1203 +(((((((....[[[[((((.....((((((((.....))))))))))))))))))).......]]]]
1204 +>>_PKB58:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK3)
1205 +AGUGUUUGUCCCUCCACUUAAAUCGAAGGG
1206 +((((.....[[[[[))))......].]]]]
1207 +>>_PKB59:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK2)
1208 +CGUGGUGCAUACGAUAAUGCAU
1209 +(((.[[[[[[)))...]]]]]]
1210 +>>_PKB60:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK3)
1211 +AGUGUUUAUCCCUCCACUUGAAUCGAAGGG
1212 +((((.....[[[[[))))......].]]]]
1213 +>>_PKB61:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK2)
1214 +CGUUGUGUACACGAUAGUACAU
1215 +(((.[[[[[[)))...]]]]]]
1216 +>>_PKB62:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK3)
1217 +AGUGGUUAUCCCUCCACUUAAAUCGAAGGG
1218 +((((.....[[[[[))))......].]]]]
1219 +>>_PKB63:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK2)
1220 +CGUGGUGCAUACGAUAAUGCAU
1221 +(((.[[[[[[)))...]]]]]]
1222 +>>_PKB65:_E.coli_(Ec_16S-PK505/526)
1223 +GCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGC
1224 +((((((((...[[[[[[[......))).......]]]]]]])))))
1225 +>>_PKB66:__(TPK-70.28)
1226 +CAAGAACCGGACGGGUGAGAACCGAGACAAACACCCACCA
1227 +.......(((..[[[[[....))).......]]]]]....
1228 +>>_PKB67:_Legionella_pneumophila_(Lp_PK1)
1229 +CGAGAAGGAGAUCUCUCGUAAAUAAGACUC
1230 +(((((..[[[.[[))))).......]]]]]
1231 +>>_PKB68:_Legionella_pneumophila_(Lp_PK2)
1232 +GUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGUAUCCCGUUCGACCGAGCCCGCUUAUCGGUAU
1233 +(((.(((....((((.[[[[[[[..........)))).....))).)))............]]]]]]]
1234 +>>_PKB69:_Legionella_pneumophila_(Lp_PK3)
1235 +CGGUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUAUGGCGCGAAACUCAGGGA
1236 +(((((((((........................[[[[[[[))))))).))...]]].]]]]
1237 +>>_PKB70:_Legionella_pneumophila_(Lp_PK4)
1238 +GCUGUGUAUCAUCCUGCCCGUCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGC
1239 +((((((..((.(((.[[[.[[[))).))..))))))...........]]]..]]]
1240 +>>_PKB72:_E.coli_(Ec_S15)
1241 +GGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAA
1242 +((((.((((((.[[[[[[[))))))))))...............................]]]]]]]
1243 +>>_PKB73:_T2_bacteriophage_(T2_gene32)
1244 +CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGC
1245 +.(((((.[[[[[[[))))).......]]]]]]]
1246 +>>_PKB74:_bacteriophage_T4_(T4_gene32)
1247 +UGCCAGCUAUGAGGUAAAGUGUCAUAGC
1248 +((((.[[[[[[[)))).....]]]]]]]
1249 +>>_PKB75:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_g)
1250 +UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCA
1251 +.(((((((..[[[[[[[{{{.[[.....}}})))))))]]....(((((((((((((...))))))))).)))).....]]]]]]]..
1252 +>>_PKB76:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_ag)
1253 +GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCACGUCCACUCGGAUGGCUAAGGGAGAGCCA
1254 +(((((((........[[[[(((.......))))))))))...(((((((....((((....))))..)))))))......]]]].....
1255 +>>_PKB78:_AKV_murine_leukemia_virus_(AKV-MuLV)
1256 +UAGGGGGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCACUGUCGGGGGGCA
1257 +...........((((((((.[[[[[[[)))).))))..................]]]]]]].
1258 +>>_PKB79:_gibbon_ape_leukemia_virus_(GaLV)
1259 +UAGGGGAGUCAGGGUUCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGGA
1260 +...........((((((((..[[[[[[[)))))))).................]]]]]]].
1261 +>>_PKB80:_mouse_mammary_tumor_virus_(MMTV_gag/pro)
1262 +AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG
1263 +..............(((((.[[[[[[[.)))))........]]]]]]].
1264 +>>_PKB81:__(oligo_PK5)
1265 +GCGAUUUCUGACCGCUUUUUUGUCAG
1266 +(((....[[[[[)))......]]]]]
1267 +>>_PKB82:_tobacco_mosaic_virus_(TMV-L_UPD-PK1)
1268 +AUAAAGUUUGUGUUUCUAAAACACAC
1269 +..(((...[[[[)))......]]]].
1270 +>>_PKB83:_tobacco_mosaic_virus_(TMV-L_UPD-PK2)
1271 +ACGUGGUACGUACGAUAACGUACA
1272 +.(((.[[[[[[)))...]]]]]].
1273 +>>_PKB84:_tobacco_mosaic_virus_(TMV-L_UPD-PK3)
1274 +CAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
1275 +.((((.....[[[[[))))......].]]]].
1276 +>>_PKB85:_tobacco_mosaic_virus_(CcTMV_UPD-PK1)
1277 +AAGUUUGGUCGUACUUAACGACCU
1278 +.(((..[[[[[[)))..]]]]]].
1279 +>>_PKB86:_tobacco_mosaic_virus_(CcTMV_UPD-PK2)
1280 +UAGGGGCUUACCGAAAUAAGCC
1281 +.(((.[[[[[)))...]]]]].
1282 +>>_PKB87:_tobacco_mosaic_virus_(CcTMV_UPD-PK3)
1283 +CCGUGUUUAAGAGUCCACGCAAAUCGAACUCU
1284 +.((((.....[[[[[))))......].]]]].
1285 +>>_PKB88:_Feline_leukemia_virus_(FeLV)
1286 +UAGGAGAGUCAGGGCCAGGACCCCCCCCCCUGAGCCCAGGAUAACCUUAAGAAUAGGGGGGC
1287 +...........((((((((...[[[[[[)))).))))..................]]]]]].
1288 +>>_PKB89:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK1)
1289 +ACCUCGAAAGCUUAGUUUCGAGGGUCUUCUGAU
1290 +.((((((((..[[[[)))))))).....]]]].
1291 +>>_PKB90:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK2)
1292 +UGGUGGUGCACACCAAAGUGCAUA
1293 +.(((.[[[[[[)))...]]]]]].
1294 +>>_PKB91:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK3)
1295 +UAGUGCUUUCCCGUUCACUUAAAUCGAACGGUU
1296 +.((((.....[[[[[))))......].]]]]..
1297 +>>_PKB92:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK1)
1298 +AAAGUCGCUGAAGACUUAAAAUUCAGG
1299 +.(((((.[[[[[)))))....]]]]].
1300 +>>_PKB93:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK2)
1301 +GGGUGGCUGAUACCAAAAUCAGCA
1302 +.(((.[[[[[[)))...]]]]]].
1303 +>>_PKB94:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK3)
1304 +CAGUGGUUGUUCGUCCACUUAAAUAUAACGAUU
1305 +.((((.....[[[[.))))........]]]]..
1306 +>>_PKB95:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK1)
1307 +AGUUGGACGAACAUUAAACGUCC
1308 +.(((.[[[[)))......]]]].
1309 +>>_PKB96:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK2)
1310 +CCGUGGCGAGUACGAUAACUCGUA
1311 +.(((.[[[[[[)))...]]]]]].
1312 +>>_PKB97:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK3)
1313 +UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
1314 +.((((.....[[[[[))))......].]]]].
1315 +>>_PKB98:_baboon_endogenous_virus_(BaEV)
1316 +UAGGGGUGUCAGGGCUCUGGAGCCCCCCCCGAGCCCCGGCUAACUCUAUCUGUAGGGGGGCA
1317 +...........((((((.((.[[[[[[[))))))))..................]]]]]]].
1318 +>>_PKB99:_Cas-Br-E_murine_leukemia_virus_(Cas-Br-E-MuLV)
1319 +UAGGGGGGUCGGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGCAA
1320 +...........((((((((.[[[[[[[)))).))))..................]]]]]]]..
1321 +>>_PKB100:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK1)
1322 +AAGCCUUUUGGAUCGAAGGUUAAACGAUCCG
1323 +.((((((..[[[[[[))))))...]]]]]].
1324 +>>_PKB101:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK2)
1325 +CGCUCCUCGCUUGAGCUUGAGGCGGC
1326 +.((((.[[[[[[))))...]]]]]].
1327 +>>_PKB102:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK3)
1328 +GCGUAUCUCUUAUGUCAACAGAGA
1329 +.((((.[[[[)))).....]]]].
1330 +>>_PKB103:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK1)
1331 +CGCCGACGUGGCUGUAUAAUACGUC
1332 +.(((.[[[[)))........]]]].
1333 +>>_PKB104:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK2)
1334 +UCGUUGACAAGUACGAAAUCUUGUUA
1335 +.(((.[[[[[[.)))....]]]]]].
1336 +>>_PKB105:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK3)
1337 +UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
1338 +.((((.....[[[[[))))......].]]]].
1339 +>>_PKB107:_simian_retrovirus-1_(SRV1_gag/pro)
1340 +GGGAAACGGACUGAGGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCG
1341 +..............((((((.[[[[[[))))))............]]]]]].
1342 +>>_PKB108:_Tetrahymena_thermophila_(T.the_telo)
1343 +UAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUA
1344 +...((((...[[[[[[[[))))....]]]]]]]].
1345 +>>_PKB109:_beet_virus_Q_(BVQ1_UPD-PKc)
1346 +UUGUGGUGCAUACAAUAAUGCAUA
1347 +.(((.[[[[[[)))...]]]]]].
1348 +>>_PKB110:_beet_virus_Q_(BVQ1_UPD-PKb)
1349 +UAGUGUUUGCCGUUCCACUUAAAUCGAAACGGA
1350 +.((((....[[[[[[))))......].]]]]].
1351 +>>_PKB111:_beet_virus_Q_(BVQ2_UPD-PKc)
1352 +ACGUGGUGCAUACGUUAAUGCAUA
1353 +.(((.[[[[[[)))...]]]]]].
1354 +>>_PKB112:_beet_virus_Q_(BVQ2_UPD-PKb)
1355 +UAGUGUUUUUCGUUCCACUUAAAUCGAAACGAU
1356 +.((((....[[[[[[))))......].]]]]].
1357 +>>_PKB113:_beet_virus_Q_(BVQ3_UPD-PKc)
1358 +UCGUGGUGCAUACGAAAAUGCAUA
1359 +.(((.[[[[[[)))...]]]]]].
1360 +>>_PKB114:_beet_virus_Q_(BVQ3_UPD-PKb)
1361 +UAGUGUUUACCGUUCCACUUAAAUCGAAACGGA
1362 +.((((....[[[[[[))))......].]]]]].
1363 +>>_PKB115:_beet_soil-borne_virus_(BSBV1_UPD-PKc)
1364 +CGGUAGCGCGAACCUUAUCGCGCA
1365 +.(((.[[[[[[)))...]]]]]].
1366 +>>_PKB116:_beet_soil-borne_virus_(BSBV1_UPD-PKb)
1367 +CAGUGUUUUGAAGUCCACUUAAAUAGAACUUCU
1368 +.((((....[[[[[[))))......].]]]]].
1369 +>>_PKB117:_beet_soil-borne_virus_(BSBV2_UPD-PKc)
1370 +ACGUGGGUUAUACGAUAAUAACCG
1371 +.(((.[[[[[[)))...]]]]]].
1372 +>>_PKB118:_beet_soil-borne_virus_(BSBV2_UPD-PKb)
1373 +CGGUGCUUUUAUGUUCACCGAAAUCGAACAUAC
1374 +.((((....[[[[[[))))......].]]]]].
1375 +>>_PKB119:_beet_soil-borne_virus_(BSBV3_UPD-PKc)
1376 +ACGUGGCGAAUACGAUAAUUCGUA
1377 +.(((.[[[[[[)))...]]]]]].
1378 +>>_PKB120:_beet_soil-borne_virus_(BSBV3_UPD-PKb)
1379 +UAGUGUUCGUGGAUAACACUUUAAUUAAGAUUCAUA
1380 +.((((((.[[[[[[)))))).........]]]]]].
1381 +>>_PKB121:_satellite_tobacco_necrosis_virus_1_(STNV1_PK1)
1382 +AAGCAGUCCCAGCUCUGCAUUGGGAA
1383 +.(((..[[[[[)))......]]]]].
1384 +>>_PKB122:_satellite_tobacco_necrosis_virus_1_(STNV1_PK2)
1385 +UACUACUUGCUCAUUUGUAGUCUAAAUGAGA
1386 +.(((((...[[[[[[[)))))..]]]]]]].
1387 +>>_PKB123:_satellite_tobacco_necrosis_virus_1_(STNV1_PK3)
1388 +GACGUUGGCCUCGACGUGUCGAGGUG
1389 +.((((..[[[[[[))))..]]]]]].
1390 +>>_PKB124:_satellite_tobacco_necrosis_virus_2_(STNV2_PK1)
1391 +CAGUAGUCCUGAACUAGUAAAUCAGGACC
1392 +.(((.[[[[[[[)))......]]]]]]].
1393 +>>_PKB125:_satellite_tobacco_necrosis_virus_2_(STNV2_PK2)
1394 +CCAUUCCCACUAGUGUAUUAGUGGA
1395 +.(((..[[[[[[)))...]]]]]].
1396 +>>_PKB126:_satellite_tobacco_necrosis_virus_2_(STNV2_PK3)
1397 +GAACGAGGCCCCGCGUGAAUUGGGGUG
1398 +..(((..[[[[[[)))....]]]]]].
1399 +>>_PKB130:_tobacco_rattle_virus_(TRV-PSG)
1400 +AGGGGUAAAACCCCUCGCCUACGUAAGCGUUAUUACGCCC
1401 +...............(((...[[[[[)))...]]]]]...
1402 +>>_PKB131:__(NGF-H1)
1403 +CGCUCAACUCAUGGAGCGCAAGACGAAUAGCUACAUAUUCGACAUGAG
1404 +(((((..[[[[[[))))).....((((((......)))))).]]]]]]
1405 +>>_PKB132:__(NGF-L2)
1406 +CGCUCAACCUCAGAGCGCAAGAGUCGAACGAAUACAGUUCGACAUGAGG
1407 +(((((..[[[[[))))).....(((((((.......))))))).]]]]]
1408 +>>_PKB133:__(NGF-L6)
1409 +CGCUCAACUCAUGGAGCGCACGACGGAUCACCAUCGAUUCGACAUGAG
1410 +(((((..[[[[[[))))).....((((((......)))))).]]]]]]
1411 +>>_PKB138:_barley_stripe_mosaic_virus_(BSMVbeta)
1412 +AUUGGUAUGUAAGCUACAACUUCCGGUAGCUGCGUCACACUUUAAGAGUGUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCCCCAAGGGAAGACCA
1413 +.((((((((..((((((..[[[[[.))))))....((((((.....)))))))))))))).((((((.....)))))).........]]]]]....
1414 +>>_PKB139:_tobacco_mosaic_virus_(TMV-L_PKbulge)
1415 +UAGUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGAG
1416 +..((((((....[[[[((((.....((((((((.....)))))))))))))))))).........]]]].
1417 +>>_PKB140:_cucumber_green_mottle_mosaic_virus_(CGMMV_PKbulge)
1418 +UUUGCUCAUUGGUUUGCGGAAACCUCUCACGUGUGACGUUGAAGUUUCUAUGGGCAGUAAUUCUGCAAG
1419 +.((((((((....[[[[((((((.((..(((.....))).)).)))))))))))))).......]]]].
1420 +>>_PKB141:_tobacco_mild_green_mosaic_virus_(TMGMV_PKbulge)
1421 +UUGUCAUAUCUGGAUCCAACAGUUAAACCAUGUGAUGGUGUAUACUGUGGUAUGGCGUAAAACAUCGGAG
1422 +.(((((((((....[[[.(((((...((((.....))))....)))))))))))))).........]]].
1423 +>>_PKB142:_satellite_tobacco_mosaic_virus_(STMV_PKbulge)
1424 +UUUUGUUUUGGUCUUCCCGAACGCAUACGUUAGUGUGACUACCGUUGUUCGAAACAAGUAAAACAGGAAGG
1425 +.(((((((....[[[[[((((((...(((.(((.....))).)))))))))))))))).......]]]]].
1426 +>>_PKB143:_pepper_mild_mottle_virus_(PMMV-S_PKbulge)
1427 +UUGUCGUUGGGAUGGAACGCAAUUAAAUACAUGUGUGACGUGUAUUUGCGAACGACGUAAUUAUUUUUCAG
1428 +.(((((((....[[[[[(((....(((((((((.....)))))))))))))))))))........]]]]].
1429 +>>_PKB144:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge1)
1430 +UUGUGUAUAUGGAUCAUGCGGAUAAAGUUAUACUGGUGCAGUAUAACCCGUUAUACACAUAAAAUUAUGAG
1431 +.((((((((....[[[[((((.....((((((((.....)))))))))))))))))))).......]]]].
1432 +>>_PKB145:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge2)
1433 +UUGUGUCAGACGCGUGUAAGGAGUGGUCAACCUUACGACACAUUUAAAUAAUGCGUCC
1434 +.(((((..[[[[[[(((((((.........)))))))))))).........]]]]]].
1435 +>>_PKB146:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge3)
1436 +UUUCACUGCGGAUAUGUAGGUUUCCUCGGUGAAUAUAAAACUUAUAUCCC
1437 +.(((((...[[[[[((.(((...))))))))))...........]]]]].
1438 +>>_PKB147:_Saccharomyces_cerevisiae_(Sc_18S-PKE21-7/8)
1439 +AUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGU
1440 +.((((((((((...[[..[[[[[[)))))))))).......]]]]]].]].
1441 +>>_PKB151:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK1)
1442 +AAAUGUUUGAUCAGAUCAUUCAAAUCUGAUGG
1443 +.((((....[[[[[[[))))...]]]]]]]..
1444 +>>_PKB152:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK2)
1445 +UGGUGCCCAUCAACCAUAUGAUGGGA
1446 +.(((.[[[[[[[)))...]]]]]]].
1447 +>>_PKB153:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK3)
1448 +GAGUGUUUGCAAGUCCACUAUAAUCGAACUUGA
1449 +.((((....[[[[[[))))......].]]]]].
1450 +>>_PKB154:_brome_mosaic_virus_(BMV3_UPD-PK1)
1451 +GAGCCCCUGACUGGGUUAAAGUCACA
1452 +.(((((.[[[[[)))))..]]]]]..
1453 +>>_PKB155:_brome_mosaic_virus_(BMV3_UPD-PK2)
1454 +CCCUUGUCUCAGGUAGAGACC
1455 +.(((.[[[[[)))..]]]]].
1456 +>>_PKB156:_brome_mosaic_virus_(BMV3_UPD-PK3)
1457 +ACUUUGGCUAAGGUUAAAAGCUU
1458 +.(((.[[[[)))......]]]].
1459 +>>_PKB157:_brome_mosaic_virus_(BMV3_UPD-PK4)
1460 +UUGUUGAAUCAGUACAAUAACUGAUA
1461 +.(((...[[[[[[)))...]]]]]].
1462 +>>_PKB158:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK1)
1463 +CUUUAAGGGACCUUGUGAAAUUCAAGGG
1464 +.((((.....[[[[[))))...]]]]].
1465 +>>_PKB159:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK2)
1466 +GGGCGGGUGUCGCCAGAAAUCACCG
1467 +.(((.[[[[[.)))....].]]]].
1468 +>>_PKB160:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK3)
1469 +CGAUACUACUAGUUGUAUCAAAACAAAACUAA
1470 +.(((((...[[[[[))))).......]]]]].
1471 +>>_PKB161:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK4)
1472 +AGGUGGAUGUUACCAUAAACAUUA
1473 +.(((.[[[[[[)))...]]]]]].
1474 +>>_PKB162:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK5)
1475 +UAAUGUCGCAGGUGGCAUUUUAAAAUAAGACCUGA
1476 +.((((((.[[[[[))))))..........]]]]].
1477 +>>_PKB163:_Homo_sapiens_(Hs_SRP-pkn)
1478 +GCCGGGCGCGGUGGCGCGUGCCUGUAGUCCCAGCUACUCGGGAGGCU
1479 +(((.((((((.[[[[.)))))).....((((.]]]]...))))))).
1480 +>>_PKB164:_poa_semilatent_virus_(PSLVbeta)
1481 +AUUGGUAUGUAAGCUACUUCUUCCAGUAGCUGCGUCAUAACAUCAAGGUUAUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCUCCAAGGAAGACCA
1482 +.((((((((..((((((..[[[[[.))))))....((((((......)))))))))))))).((((((.....))))))........]]]]]....
1483 +>>_PKB165:_poa_semilatent_virus_(PSLVbeta_UPD-PK1)
1484 +AUUGCCACUGUGGAAAUCAGUGA
1485 +.(((.[[[[[)))....]]]]].
1486 +>>_PKB166:_poa_semilatent_virus_(PSLVbeta_UPD-PK2)
1487 +CGGUUUUAUCUACCAUAAGAUAAA
1488 +.(((.[[[[[[)))...]]]]]].
1489 +>>_PKB167:_poa_semilatent_virus_(PSLVbeta_UPD-PK3)
1490 +AAGUGUUUUCAUGUCCACUUAAAUCGAACAUGAAC
1491 +.((((..[[[[[[[[))))......].]]]]]]].
1492 +>>_PKB169:_Coxsackie_B_virus_(CoxB3)
1493 +ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAAAAAA
1494 +.((((((((((((.[[[[[[.........)))))))))))).....((.(((((.]]]]]]))))).))....
1495 +>>_PKB172:_bamboo_mosaic_virus_(BaMV)
1496 +CUUUUGGUUUCUACAGUUUUUUCCAAAAAAAAAAAAAAA
1497 +.((((((.........[[[[[[))))))...]]]]]]..
1498 +>>_PKB173:_Satellite_cereal_yellow_dwarf_virus-RPV_RNA_(satRPV)
1499 +ACAGAGCGCGUACUGUCUGACGACGUAUCCGCGCGGACUAGAAGGCUGGUGCCUCGUCCAACAAAUAGAUACA
1500 +((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))).
1501 +>>_PKB175:__(biotin-PK)
1502 +CACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGC
1503 +.(((((.[[[[[[[)))))..............................]]]]]]].
1504 +>>_PKB176:__(biotin-PK-AN69.1)
1505 +GGACCGUCAGAGGACACGGUUAAAAAGUCCUCU
1506 +..(((((..[[[[[[)))))......]]]]]].
1507 +>>_PKB177:_Rattus_rattus_(black_rat)_(Rr_ODCanti)
1508 +UGCUCCUGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAACAGUCAGCGGGAUCACAGU
1509 +............(((((.((((((......[[[[[[.)))))).)))))..........]]]]]].....
1510 +>>_PKB182:_soil-borne_rye_mosaic_virus_(SBRMV1-PKa)
1511 +GGGGUUCAAAUCCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
1512 +...............(((....[[[[[)))...]]]]]....
1513 +>>_PKB183:_soil-borne_rye_mosaic_virus_(SBRMV1-UPD-PKb)
1514 +ACGUCGUGCAGUACGGUAAACUGCACA
1515 +.(((.[[[[[[[)))....]]]]]]].
1516 +>>_PKB184:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKc)
1517 +UUCUGUUUUUCGAACAGAUGUAAAUCGAAGA
1518 +.(((((.[[[[[[)))))......]]]]]].
1519 +>>_PKB185:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKd)
1520 +ACGUGGCCAUCACGAUAGAUGGUU
1521 +.(((.[[[[[[)))...]]]]]].
1522 +>>_PKB186:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKe)
1523 +AAGCCUAUUUGUACGGGUUGAGUACAAAC
1524 +.(((((.[[[[[..)))))....]]]]].
1525 +>>_PKB187:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKf)
1526 +GCCGCUGGGAUUGCGGAUUAUAAAUCG
1527 +.((((...[[[[))))......]]]].
1528 +>>_PKB188:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKg)
1529 +UCGUUGCCGUCACGAUAGACGGA
1530 +.(((..[[[[[)))...]]]]].
1531 +>>_PKB189:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKh)
1532 +AGUCUAACAUGUCGGGCUGAGACAUGUC
1533 +.((((.[[[[[[[))))...]]]]]]].
1534 +>>_PKB190:_Plautia_stali_intestine_virus_(PSIV_IRES)
1535 +CUCGCUCAAACAUUAAGUGGUGUUGUGCGAAAAGAAUCUCACUUCAA
1536 +.((((...(((((.[[[[[)))))..)))).........]]]]]...
1537 +>>_PKB194:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKb)
1538 +UACGCUGUACAGUGCGUUAAACUGUACA
1539 +..(((.[[[[[[[)))....]]]]]]].
1540 +>>_PKB195:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKc)
1541 +CUCUGUUGAUCAAACAGAAAUAAAUUGAUUA
1542 +.(((((.[[[[[[)))))......]]]]]].
1543 +>>_PKB196:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKd)
1544 +ACGCGGUCAUUGCGAUAAAUGACU
1545 +.(((.[[[[[[)))...]]]]]].
1546 +>>_PKB197:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKe)
1547 +GAACCUAUUUGCUCGGGUUGAGUGCAAAC
1548 +..((((.[[[[[..)))).....]]]]].
1549 +>>_PKB198:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKf)
1550 +ACCGCCUGAUUAGCGGUCUACAAGUUAAUCGA
1551 +.((((..[[[[[)))).........]]]]]..
1552 +>>_PKB199:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKg)
1553 +UCGUGGUCAGUACGAUAACUGAU
1554 +.(((..[[[[[)))...]]]]].
1555 +>>_PKB200:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKh)
1556 +AGUCUAAUUUGUCGGGCUGAGACAAAUC
1557 +.((((.[[[[[[[))))...]]]]]]].
1558 +>>_PKB201:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKb)
1559 +GGCGUUCUACAGUACGUUUAAACUGUAGG
1560 +..(((.[[[[[[[))).....]]]]]]].
1561 +>>_PKB202:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKi)
1562 +UGGUGCUUGUUAUUUCACCUAAAUCGAAAUAACG
1563 +.((((...[[[[[[[)))).......]]]]]]].
1564 +>>_PKB203:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKk)
1565 +ACGUGGUCUUCACGAUAGAAGAUG
1566 +.(((.[[[[[[)))...]]]]]].
1567 +>>_PKB204:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKl)
1568 +CAGAGUUAUCAUACUCUAUAAACUAUGAC
1569 +.((((...[[[[[))))......]]]]].
1570 +>>_PKB205:_Palmaria_palmata_(Pp_18S-PKE23-9/12)
1571 +UUAGAGUGUUCAAAGCCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAA
1572 +.((..((.[[[[..))(((((....))).))..))........]]]].
1573 +>>_PKB206:_Homo_sapiens_(Hs_PrP)
1574 +GCCUCAUGGUGGUGGCUGGGGGCAGCCUCAUGGUGGUGGCUGGGG
1575 +...((((((.............[[[[[))))))....]]]]]...
1576 +>>_PKB207:_Bos_Taurus_(cow)_(Bt_PrP)
1577 +GCCCCAUGGAGGUGGCUGGGGCCAGCCUCAUGGAGGUGGCUGGGG
1578 +...((((((............[[[[[[))))))....]]]]]]..
1579 +>>_PKB210:_Bordetella_pertussis_(Bp_PK2)
1580 +CCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCAACUUCCCAGGGGGCAACCCCGAACCGCAGCAGCGACAUUCACAAGGAAU
1581 +.((((((..(((...[[[[[[[..))).((((((((((....)))))).((((....))))...)))).)))))).......]]]]]]].
1582 +>>_PKB212:_Plautia_stali_intestine_virus_(PSIV_IRES-PKIII)
1583 +AGGUCUUGUAUAUUUAUACUUACCACACAAGAUGGACCGGAGCAGCCCUCCAAUAUCUAGUGUA
1584 +.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
1585 +>>_PKB213:_Himetobi_P_virus_(HiPV_IRES-PKI)
1586 +CAGCCUUGUAGUUUUAGUGGACUUUAGGCUAAAGAAUUUCACUAG
1587 +.(((((...((((.[[[[[))))..))))).........]]]]].
1588 +>>_PKB215:_Himetobi_P_virus_(HiPV_IRES-PKIII)
1589 +GACCCUUAGUUAUUUAGCUUUACCGCCCAGGAUGGGGUGCAGCGUUCCUGCAAUAUCCAGGGCA
1590 +.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
1591 +>>_PKB216:_Drosophila_C_virus_(DCV_IRES-PKI)
1592 +CUUCUUAUAUGAUUAGGUUGUCAUUUAGAAUAAGAAAAUAACCUG
1593 +.((((...(((((.[[[[[)))))..)))).........]]]]].
1594 +>>_PKB218:_Porcine_reproductive_and_respiratory_syndrome_virus,_North_American_isolate_(16244B)_(PRRSV-16244B)
1595 +UUUAAACUGCUAGCCGCCAGCGGCUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAGACAGCGGUA
1596 +............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]]..
1597 +>>_PKB220:_Drosophila_C_virus_(DCV_IRES-PKIII)
1598 +UUAGGUUAACUAUUUAGUUUUACUGUUCAGGAUGCCUAUUGGCAGCCCCAUAAUAUCCAGGACA
1599 +.((((..((((....)))).....[[[[.[[[[[)))).(((.....)))...]]]]].]]]].
1600 +>>_PKB221:_Cricket_paralysis_virus_(CrPV_IRES-PKI)
1601 +CGGUUUUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUG
1602 +.((((((...(((.[[[[[)))..)))))).........]]]]].
1603 +>>_PKB223:_Cricket_paralysis_virus_(CrPV_IRES-PKIII)
1604 +UUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAGUGGCAGCCCCACAAUAUCCAGGAAG
1605 +.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
1606 +>>_PKB224:_Triatoma_virus_(TrV_IRES-PKI)
1607 +UUUCCUAUACCUCGAGUCGGGUUUGGAAUCUAAGGUUGACUCG
1608 +.((((...((((.[[[[[))))..)))).........]]]]].
1609 +>>_PKB226:_Triatoma_virus_(TrV_IRES-PKIII)
1610 +UGCGCUUGCCUAUUUAGGCAUACUUCUCAGGAUGGCGCGUUGCAGUCCAACAAGAUCCAGGGAC
1611 +.((((..((((....)))).....[[[[.[[[[.))))((((.....))))...]]]].]]]].
1612 +>>_PKB227:_Black_queen_cell_virus_(BQCV_IRES-PKI)
1613 +AUGUUUAGAAGAUUAGGUAGUCUCUAAACAGAACAAUUUACCUG
1614 +.(((((...((((.[[[[[))))..)))))........]]]]].
1615 +>>_PKB229:_Black_queen_cell_virus_(BQCV_IRES-PKIII)
1616 +AUCACCGUACCUAUUUAGGUUUACGCUCCAAGAUCGGUGGAUAGCAGCCCUAUCAAUAUCUAGGAGA
1617 +..((((..((((....)))).....[[[[.[[[[.))))(((((.....)))))...]]]].]]]].
1618 +>>_PKB230:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKI)
1619 +CAGGAGAGCAUACGCUAGGUCGCGUUGACUAUCCUUAUAUAUGACCUG
1620 +.((((.((((.((((.[[[[[)))))).)).)))).......]]]]].
1621 +>>_PKB232:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKIII)
1622 +UUGGUUAGCUAUUUAGCUUUACUAAUCAAGACGCCGUCGUGCAGCCCACAAAAGUCUAGAUA
1623 +.(((..((((....))))......[[[.[[[[.)))..(((.....)))....]]]].]]].
1624 +>>_PKB233:_Porcine_reproductive_and_respiratory_syndrome_virus,_European_Lelystad_strain_(LV)_(PRRSV-LV)
1625 +UUUAAACUGUUAGCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGGU
1626 +............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]].
1627 +>>_PKB234:_Variovorax_paradoxus_(Vp_PK2)
1628 +GCCUUGCAACAGUUGGCCGAUGGGCUGGGCAAGGGGGUCUGGAGCAAUCCUGACCUCCCGGCUGCAAGGAUAACUACAUGGGCU
1629 +.((((((..(((...[[[[[[[..))).(((((((((((((((....))))))))))))))).)))))).......]]]]]]].
1630 +>>_PKB235:_Giardiavirus_(GLV_IRES)
1631 +GGAGACCCAUGGAGAGUCUCCAGAGGUUCCUAAGGCCUCGAUCGCGCCUGCCGGGAGGCAGAAUGUCCCGGUUCUCC
1632 +((((((....[[[[[)))))).(((((.......)))))..........(((((((.........)))))))]]]]]
1633 +>>_PKB237:_West_Nile_virus_(WNV_PK3end)
1634 +ACCUGGGAUAGACUAGGGGAUCUUCUGCUCUGCACAACCAGCCACACGGCACAGUGCGCCGACAUAGGUGGCUGGUGGUGCUAGAACACAGGAUCU
1635 +.(((((..[[[[)))))......]]]].(((((((.(((((((((.((((.......))))......))))))))).)))).)))...........
1636 +>>_PKB238:_Dengue_virus_type_2_(DEN2_PK1)
1637 +AUGGGGGCCCAAGGUGAGAUGAAGCUGUAGUCUCACUGGAAGGACUAGAGGUUAGAGGAGACCCCCCCAAAACAAAAAACAGCA
1638 +.((((((((...((((((((...[[[[[.))))))))....))......((((......)))))))))).........]]]]].
1639 +>>_PKB240:_beet_chlorosis_virus_(BChV)
1640 +GGGAAAUGGACUGAGCGGCGCCGACCGCCAAACAACCGGCA
1641 +..............((((.[[[[.))))........]]]].
1642 +>>_PKB241:_Montana_Myotis_leukoencephalitis_virus_(MMLV_PKb)
1643 +AGAGAGUUAUUCGCUCCUCUCGAGAUUGAGCGGC
1644 +.(((((....[[[[[[)))))......]]]]]].
1645 +>>_PKB242:_Rio_Bravo_virus_(RBV_PKb)
1646 +UGAGGUUUUUCCCCUCCCUCAUGAUGAGGGGAAG
1647 +.((((...[[[[[[[[)))).....]]]]]]]].
1648 +>>_PKB244:_hepatitis_A_virus_(HAV)
1649 +UUAAACAAAUUUUCUUAAAAUUUCUGAGGUUUGUUUAUUUCUUUUAUCAGUAAAU
1650 +.((((((((((.........[[[[[[[)))))))))).........]]]].]]].
1651 +>>_PKB245:_Human_Parechovirus_1_(HPeV1)
1652 +CCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCC
1653 +.((((((..[[[[[)))))).........]]]]].
1654 +>>_PKB247:_Nemesia_ring_necrosis_virus_(NeRNV_PKa)
1655 +CCCCUGUCCCGGGUAGGGAACC
1656 +.(((..[[[[)))..]]]]...
1657 +>>_PKB248:_Nemesia_ring_necrosis_virus_(NeRNV_PKb)
1658 +UGUUCCUUGGAUUGCUACGUUCACCAGAUUUGUGUAAUCUGGCCGUUAGGAACUUAAAAUUGCGCG
1659 +.((((((.....[[[((((....(((((((.....))))))).))))))))))........]]]..
1660 +>>_PKB249:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK1)
1661 +UAGUGUUUCGGCUUCCACUUAAAUCGAAAGCCA
1662 +.((((....[[[[[[))))......].]]]]].
1663 +>>_PKB250:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK2)
1664 +GGGUGGCGCACACCACAGUGCGUA
1665 +.(((.[[[[[[)))...]]]]]].
1666 +>>_PKB251:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK3)
1667 +CAGCCUCUCACAGCUUCCUCGUGAGG
1668 +.(((..[[[[[.))).....]]]]].
1669 +>>_PKB253:_White_Bream_Virus_(WBV)
1670 +UUUAAACUGGUGGGGCAGUGUCUAGGAUUGACGUUAGACACUGCUUUUUGCCCGUUUCAAACAGGUGAAUACAAACCGUCAU
1671 +...........((((((((((((((...[[[[[)))))))))))))).............................]]]]].
1672 +>>_PKB254:_SARS_coronavirus_(SARS-CoV)
1673 +UUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCUU
1674 +............(((((((((((...[[[[[[[)))))))))))((((((((.........))).)))))...]].]]]]].
1675 +>>_PKB255:_mouse_hepatitis_virus_(MHV)
1676 +CUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGA
1677 +.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
1678 +>>_PKB256:_bovine_coronavirus_(BCV)
1679 +CUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGA
1680 +.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
1681 +>>_PKB257:_Mus_musculus_(mouse)_(Mm_Edr)
1682 +GGGAAACUCCCCGGCCCCGCUGUAGGGGGACCUUCAGCGACAGGGCCAGAACGAAUAAGGUCCCCA
1683 +............((((((((((...[[[[[[[[[)))))...))))).........]]]]]]]]].
1684 +>>_PKB258:_Homo_sapiens_(Hs_Ma3)
1685 +GGGAAACGGGAACUGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAAGUAGGCUCG
1686 +.............(((((((((((...[[[[[.)))))))))))..........]]]]].
1687 +>>_PKB259:_potato_yellow_vein_virus_(PYVV1)
1688 +CGGUAGAAAAGAUGGUUUAAACCACGCCUUCUACCAAGUUAGUAAAUAAAUAGGCGG
1689 +.((((((.....((((....))))[[[[[))))))................]]]]].
1690 +>>_PKB260:_potato_yellow_vein_virus_(PYVV2)
1691 +AGUAGAAAAGUUGGUGCUUAGACCACGCCCUCUACCGUAAUAAUAGAUAAAUAGGCG
1692 +.(((((.....((((......))))[[[[.)))))..................]]]]
1693 +>>_PKB261:_potato_yellow_vein_virus_(PYVV3)
1694 +CGGUAGAAAAGAUGGUUUGAAAACCACGCCUUCUACCAAUAUAGUAAAUAAAUAGGCGG
1695 +.((((((.....(((((....)))))[[[[[))))))................]]]]].
1696 +>>_PKB262:_cucumber_yellows_virus_(CuYV1)
1697 +CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
1698 +.((((((((...((((.....)))).[[[))))))))................]]]
1699 +>>_PKB263:_cucurbit_yellow_stunting_disorder_virus_(CYSDV1)
1700 +CGACACUCUAAAGAGUUCCGUGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
1701 +.(((((((......(((((....))))).[[[[.)))))))................]]]].
1702 +>>_PKB264:_cucurbit_yellow_stunting_disorder_virus_(CYSDV2)
1703 +CGACACUCUAAAGUGUUCCAAGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
1704 +.(((((((......(((((....))))).[[[[.)))))))................]]]].
1705 +>>_PKB265:_sweet_potato_chlorotic_stunt_virus_(SPCSV1)
1706 +CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
1707 +.((((((((.....((((....))))[[[[[.))))))))................]]]]]
1708 +>>_PKB266:_lettuce_infectious_yellows_virus_(LIYV1)
1709 +UGUCUUCCUAAAAUCCUUGGAAGACUGUAUAUAUAGAAUAAAGGUCG
1710 +.(((((((......[[[[)))))))...............]]]]...
1711 +>>_PKB267:_little_cherry_virus_1_(LChV-1)
1712 +AAUGCAACUUUUAAAUAGUUUAUCUGUUAAGAUAAACCACCUAGGUUGCAUAUAUAAAAAAUAAAAGGUGCC
1713 +.(((((((((.......((((((((....))))))))[[[[[)))))))))..............]]]]]..
1714 +>>_PKB268:_beet_yellows_virus_(BYV)
1715 +CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
1716 +.(((((((...[[[[.)))))))...........]]]]..
1717 +>>_PKB269:_citrus_tristeza_virus_(CTV)
1718 +AGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACGCACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
1719 +.(((((((.......((((((((......))))))))....[[[[[)))))))....]]]]]....
1720 +>>_PKB270:_Pineapple_mealybug_wilt_associated_virus_-_2_(PMWaV-2)
1721 +CAAAGUCCUAUAAACCUCAAUAAUCCCUCGUUAGGAGGGACACGCGAGGACUUUGGCGUGCC
1722 +.((((((((..............((((((.....))))))[[[[[.)))))))).]]]]]..
1723 +>>_PKB271:_Grapevine_leafroll-associated_virus_-_2_(GLRaV-3)
1724 +ACGCCAAAAUCCAAUUAAAGUUUGGGACCUAGGCGGGCCUCUUACGAGGCUAACUUAUCGACAAUAAGUUAGGUC
1725 +.((((.....((((.......))))[[[[[[))))((((((....))))))..................]]]]]]
1726 +>>_PKB272:_strawberry_chlorotic_fleck_associated_virus_(SCFaV)
1727 +ACUGUGAUUAUAAAAGUGGAGUACUAAAGUACCCACUACCUUUAAUCACAGACAAUAAAGGUCCAU
1728 +.((((((((.....(((((.((((....)))))))))[[[[[[)))))))).....]]]]]]....
1729 +>>_PKB273:_influenza_A_virus,_strain_A/PR/8/34_(IAV_PK_NS)
1730 +UUCCAGGACAUACUGCUGAGGAUGUCAAAAAUGCAGUUGGAGUCCUCA
1731 +.(((((...........[[[[[[.............)))))]]]]]].
1732 +>>_PKB274:_influenza_B_virus,_strain_B/Victoria/02/1987_(IBV_PK_NS)
1733 +ACUGAUGAUCUUACAGUGGAGGAUGAAGAAGAUGGCCAUCGGAUCCUCA
1734 +.((((((...........[[[[[[............))))))]]]]]].
1735 +>>_PKB275:_Bacillus_subtilis_(Bs_glmS_P3.1)
1736 +CCGGCUGAGUGUGCAGAUCACAGCCGUAAGAAUUUCUUCAAACCAAGGGGGUGACUCCUUGAACAAAGAGAAAUCACAUGAUCUU
1737 +.((((((.......[[[[[[)))))).....(((((((.....(((((((....)))))))......)))))))....]]]]]].
1738 +>>_PKB276:_Bacillus_subtilis_(Bs_glmS_P1.1)
1739 +CGCCCGAACUAAGCGCCCGGAAAAAGGCUUAGUUGACGAGGAUGGAGGUUAUCGAAUUUCGCGGAUCCUCCCG
1740 +.(((((((((((((............)))))))).........[[[[[....(((...))))))))]]]]]..
1741 +>>_PKB277:_tobacco_etch_virus_(TEV_PK1)
1742 +CGAAUCUCAAGCAAUCAAGCAUUCUACUUCUAUUGCA
1743 +.((((((...[[[[[..)).)))).......]]]]].
1744 +>>_PKB278:_tobacco_etch_virus_(TEV_PK2)
1745 +AUUUAAAUCAUUUCUUUUAAAGCAAAAGC
1746 +.((((((...[[[..))))))....]]].
1747 +>>_PKB279:_tobacco_etch_virus_(TEV_PK3)
1748 +CAAUUUUCUGAAAAUUUUCAC
1749 +.(((((..[[[))))).]]].
1750 +>>_PKB280:_Visna-Maedi_virus_(VMV)
1751 +GGGAAACAACAGGAGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGUUGUAACAGAAGCACCACC
1752 +.............(((((((.....[[[[[[[.......)))))))..............]]]]]]].
1753 +>>_PKB281:_sugarcane_yellow_leaf_virus_(ScYLV)
1754 +GGGAAACGAGCCAAGUGGCGCCGACCACUUAAAAACACCGGAA
1755 +.............(((((..[[[.))))).........]]]..
1756 +>>_PKB282:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKI)
1757 +CCGUCGUUUCCGACGUAAAAGGAAGCAA
1758 +.((((..[[[[)))).....]]]]....
1759 +>>_PKB283:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKII)
1760 +CCGCCUGUCCCGGCGUUAAAGGGAAGUAA
1761 +.((((..[[[[)))).....]]]].....
1762 +>>_PKB284:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKIII)
1763 +ACCGCCUACCCCGGCGUUAACGGGGAACAA
1764 +..((((..[[[[)))).....]]]].....
1765 +>>_PKB285:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKI)
1766 +ACCGUCGUUCCCGACGUAAAAGGGAGG
1767 +..((((..[[[[)))).....]]]]..
1768 +>>_PKB286:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKII)
1769 +ACCGUCCGGCCCGACGUAAAAGGGUGGUAA
1770 +..((((...[[[)))).....]]]......
1771 +>>_PKB287:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIII)
1772 +CCGUCUUUCCCGACGUUAAAGGGAUG
1773 +.((((..[[[[)))).....]]]]..
1774 +>>_PKB288:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIV)
1775 +CCUUCGCUCGGAAGUAAAACGACAA
1776 +.((((..[[[)))).....]]]...
1777 +>>_PKB289:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKI)
1778 +ACCGUCGUUCCCGACGUAAAAGGGAUGU
1779 +..((((..[[[[)))).....]]]]...
1780 +>>_PKB290:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKII)
1781 +ACCGUCUCUCCCGACGUUAAAGGGAUGUAA
1782 +..((((..[[[[)))).....]]]].....
1783 +>>_PKB291:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIII)
1784 +CCGCCUAUCCCGGCGUUAAUGGGAGG
1785 +.((((..[[[[)))).....]]]]..
1786 +>>_PKB292:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIV)
1787 +CCUUCACCUGGAAGUAAAACAGCAA
1788 +.((((..[[[)))).....]]]...
1789 +>>_PKB293:_encephalomyocarditis_virus_(EMCV-R_PKB)
1790 +ACGUGAAGGCUACGAUAGUGCCAG
1791 +.((((..[[[)))).....]]]..
1792 +>>_PKB294:_encephalomyocarditis_virus_(EMCV-R_PKC)
1793 +AGGGCGGGUACUGCCGUAAGUGCCA
1794 +..(((.[[[[[[)))...]]]]]].
1795 +>>_PKB295:_Mengovirus_(Mengo_PKB)
1796 +ACGUGAAGGCUACGAUAGUGCCAG
1797 +.((((..[[[)))).....]]]..
1798 +>>_PKB296:_Mengovirus_(Mengo_PKC)
1799 +AGGGCGGGUCCUGCCGAAAGUGCCAA
1800 +..(((.[[[.[[)))...]].]]]..
1801 +>>_PKB297:_hepatitis_A_virus_(HAV_PK1)
1802 +AAGUCCAUGGUGAGGGGACUUGAUACCUCACCG
1803 +.(((((..[[[[[[[))))).....]]]]]]].
1804 +>>_PKB298:_hepatitis_A_virus_(HAV_PK2)
1805 +CGCCGUUUGCCUAGGCUAUAGGCUAAAUU
1806 +.(((....[[[[[)))..]]]]]......
1807 +>>_PKB299:_Theiler's_murine_encephalomyelitis_virus_(TMEV)
1808 +ACGCGGGUACUGCGAUAGUGCCACC
1809 +.(((.[[[[[[)))..]]]]]]...
1810 +>>_PKB300:__(antiHIV1-RT_1.1)
1811 +UCAAGAAUUCCGUUUUCAGUCGGGAAAAACUGAACAA
1812 +.......(((((..[[[[[[)))))...]]]]]]...
1813 +>>_PKB301:__(antiHIV1-RT_1.3a)
1814 +GAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCAUCU
1815 +.......(((((..[[[[..)))))....]]]]....
1816 +>>_PKB302:__(antiHIV1-NC_psi-50-1)
1817 +GCCAGUGGUUUGCAAUGCUGGUCCGGUGCGU
1818 +(((((((...[[[[.)))))))....]]]].
1819 +>>_PKB303:_Bombyx_mori_(R2_retroPK)
1820 +AGCCCCGAUGGACGGACCGCGAGGACCGUCAAGCCUAGCAGGUACCUUCGGGUGGGGCCUUGCGAUACCUGCGGGC
1821 +.(((((....(((((.((....)).)))))...[[[.[[[[[[(((....))))))))........]]]]]]]]].
1822 +>>_PKB304:_B._subtilis_(SBU)
1823 +AGAGGUUCUAGCUACACCCUCUAUAAAAAACUAA
1824 +(((((...[[[......)))))........]]].
1 -
2 -
3 -@article{cruz2011sequence,
4 - title={Sequence-based identification of 3D structural modules in RNA with RMDetect},
5 - author={Cruz, Jos{\'e} Almeida and Westhof, Eric},
6 - journal={Nature methods},
7 - volume={8},
8 - number={6},
9 - pages={513},
10 - year={2011},
11 - publisher={Nature Publishing Group}
12 -}
13 -
14 -@article{djelloul_automated_2008,
15 - title = {Automated motif extraction and classification in {RNA} tertiary structures},
16 - volume = {14},
17 - issn = {1355-8382, 1469-9001},
18 - url = {http://rnajournal.cshlp.org/content/14/12/2489},
19 - doi = {10.1261/rna.1061108},
20 - abstract = {We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs. We identified 10 known motifs without any prior knowledge of their shapes or positions. We additionally identified four putative new motifs.},
21 - language = {en},
22 - number = {12},
23 - urldate = {2018-10-04},
24 - journal = {RNA},
25 - author = {Djelloul, Mahassine and Denise, Alain},
26 - month = jan,
27 - year = {2008},
28 - pmid = {18957493},
29 - keywords = {clustering, graph similarity, RNA tertiary structure},
30 - pages = {2489--2497},
31 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/6PDZZRI6/Djelloul et Denise - 2008 - Automated motif extraction and classification in R.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/28T5ICXG/2489.html:text/html}
32 -}
33 -
34 -@article{roll_jar3d_2016,
35 - title = {{JAR}3D {Webserver}: {Scoring} and aligning {RNA} loop sequences to known 3D motifs},
36 - volume = {44},
37 - issn = {0305-1048},
38 - shorttitle = {{JAR}3D {Webserver}},
39 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987954/},
40 - doi = {10.1093/nar/gkw453},
41 - abstract = {Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson–Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time.},
42 - number = {Web Server issue},
43 - urldate = {2018-10-04},
44 - journal = {Nucleic Acids Research},
45 - author = {Roll, James and Zirbel, Craig L. and Sweeney, Blake and Petrov, Anton I. and Leontis, Neocles},
46 - month = jul,
47 - year = {2016},
48 - pmid = {27235417},
49 - pmcid = {PMC4987954},
50 - pages = {W320--W327},
51 - file = {PubMed Central Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/KWD59J5I/Roll et al. - 2016 - JAR3D Webserver Scoring and aligning RNA loop seq.pdf:application/pdf}
52 -}
53 -
54 -@article{zhong_rnamotifscan:_2010,
55 - title = {{RNAMotifScan}: automatic identification of {RNA} structural motifs using secondary structural alignment},
56 - volume = {38},
57 - issn = {0305-1048},
58 - shorttitle = {{RNAMotifScan}},
59 - url = {https://academic.oup.com/nar/article/38/18/e176/1069222},
60 - doi = {10.1093/nar/gkq672},
61 - abstract = {Abstract. Recent studies have shown that RNA structural motifs play essential roles in RNA folding and interaction with other molecules. Computational identifi},
62 - language = {en},
63 - number = {18},
64 - urldate = {2018-10-04},
65 - journal = {Nucleic Acids Research},
66 - author = {Zhong, Cuncong and Tang, Haixu and Zhang, Shaojie},
67 - month = oct,
68 - year = {2010},
69 - pages = {e176--e176},
70 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/ESXL69Q6/Zhong et al. - 2010 - RNAMotifScan automatic identification of RNA stru.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/MWTNC94Z/1069222.html:text/html}
71 -}
72 -
73 -@inproceedings{tahi_fast_2003,
74 - title = {A fast algorithm for {RNA} secondary structure prediction including pseudoknots},
75 - doi = {10.1109/BIBE.2003.1188924},
76 - abstract = {Many important RNA molecules contain pseudoknots, which are generally excluded by the definition of the secondary structure, mainly for computational reasons. Still, most existing algorithms for secondary structure prediction are not satisfactory in results and complexities, even when pseudoknots are not allowed. We present an algorithm, called P-DCFold, for the prediction of RNA secondary structures including all kinds of pseudoknots. It is based on the comparative approach. The helices are searched recursively, from more "likely" to less "likely", using the "Divide and Conquer" approach. This approach, which allows to limit the amount of searching, is possible when only non-interleaved helices are searched for. The pseudoknots are therefore searched in several steps, each helix of the pseudoknot being selected in a different step. P-DCFold has been applied to tmRNA and RnaseP sequences. In less than two seconds, their respective secondary structures, including their pseudoknots, have been recovered very efficiently.},
77 - booktitle = {Third {IEEE} {Symposium} on {Bioinformatics} and {Bioengineering}, 2003. {Proceedings}.},
78 - author = {Tahi, F. and Engelen, S. and Regnier, M.},
79 - month = mar,
80 - year = {2003},
81 - keywords = {2 s, Bioinformatics, Biological control systems, computational methods, computational reasons, Context modeling, Databases, Evolution (biology), fast algorithm, macromolecules, molecular biophysics, molecular configurations, noninterleaved helices, Predictive models, pseudoknots, recursive searches, RNA, RNA secondary structure prediction, RnaseP, Robustness, secondary structures, spatial structures, Stochastic processes, Switches, tmRNA},
82 - pages = {11--17},
83 - file = {IEEE Xplore Abstract Record:/nhome/siniac/lbecquey/Zotero/storage/HTHXNSVF/1188924.html:text/html}
84 -}
85 -
86 -@article{tahi_p-dcfold_2005,
87 - title = {P-dcfold or how to predict all kinds of pseudoknots in rna secondary structures},
88 - volume = {14},
89 - issn = {0218-2130},
90 - url = {https://www.worldscientific.com/doi/abs/10.1142/S021821300500234X},
91 - doi = {10.1142/S021821300500234X},
92 - abstract = {Pseudoknots play important roles in many RNAs. But for computational reasons, pseudoknots are usually excluded from the definition of RNA secondary structures. Indeed, prediction of pseudoknots increase very highly the complexities in time of the algorithms, knowing that all existing algorithms for RNA secondary structure prediction have complexities at least of O(n3). Some algorithms have been developed for searching pseudoknots, but all of them have very high complexities, and consider generally particular kinds of pseudoknots.We present an algorithm, called P-DCFold based on the comparative approach, for the prediction of RNA secondary structures including all kinds of pseudoknots. The helices are searched recursively using the "Divide and Conquer" approach, searching the helices from the "most significant" to the "less significant". A selected helix subdivide the sequence into two sub-sequences, the internal one and a concatenation of the two externals. This approach is used to search non-interleaved helices and allows to limit the space of searching. To search for pseudoknots, the processing is reiterated. Therefore, each helix of the pseudoknot is selected in a different step.P-DCFold has been applied to several RNA sequences. In less than two seconds, their respective secondary structures, including their pseudoknots, have been recovered very efficiently.},
93 - number = {05},
94 - urldate = {2018-10-02},
95 - journal = {International Journal on Artificial Intelligence Tools},
96 - author = {Tahi, Fariza and Stefan, Engelen and Regnier, Mireille},
97 - month = oct,
98 - year = {2005},
99 - pages = {703--716},
100 - file = {Snapshot:/nhome/siniac/lbecquey/Zotero/storage/GEIBPMJ4/S021821300500234X.html:text/html}
101 -}
102 -
103 -@article{tempel_fast_2012,
104 - title = {A fast ab-initio method for predicting {miRNA} precursors in genomes},
105 - volume = {40},
106 - issn = {0305-1048},
107 - url = {https://academic.oup.com/nar/article/40/11/e80/2409259},
108 - doi = {10.1093/nar/gks146},
109 - abstract = {Abstract. miRNAs are small non coding RNA structures which play important roles in biological processes. Finding miRNA precursors in genomes is therefore an i},
110 - language = {en},
111 - number = {11},
112 - urldate = {2018-10-02},
113 - journal = {Nucleic Acids Research},
114 - author = {Tempel, Sébastien and Tahi, Fariza},
115 - month = jun,
116 - year = {2012},
117 - pages = {e80--e80},
118 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/BSCSRRL2/Tempel et Tahi - 2012 - A fast ab-initio method for predicting miRNA precu.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/ZTG4GDDT/2409259.html:text/html}
119 -}
120 -
121 -@article{reinharz_towards_2012,
122 - title = {Towards 3D structure prediction of large {RNA} molecules: an integer programming framework to insert local 3D motifs in {RNA} secondary structure},
123 - volume = {28},
124 - issn = {1367-4803},
125 - shorttitle = {Towards 3D structure prediction of large {RNA} molecules},
126 - url = {https://academic.oup.com/bioinformatics/article/28/12/i207/269345},
127 - doi = {10.1093/bioinformatics/bts226},
128 - abstract = {Abstract. Motivation: The prediction of RNA 3D structures from its sequence only is a milestone to RNA function analysis and prediction. In recent years, many},
129 - language = {en},
130 - number = {12},
131 - urldate = {2018-10-01},
132 - journal = {Bioinformatics},
133 - author = {Reinharz, Vladimir and Major, François and Waldispühl, Jérôme},
134 - month = jun,
135 - year = {2012},
136 - pages = {i207--i214},
137 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/IAYRK53E/Reinharz et al. - 2012 - Towards 3D structure prediction of large RNA molec.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/SSMTN6YZ/269345.html:text/html}
138 -}
139 -
140 -@article{pan_predicting_nodate,
141 - title = {Predicting {RNA}–protein binding sites and motifs through combining local and global deep convolutional neural networks},
142 - url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty364/4990826},
143 - doi = {10.1093/bioinformatics/bty364},
144 - abstract = {AbstractMotivation. RNA-binding proteins (RBPs) take over 5–10\% of the eukaryotic proteome and play key roles in many biological processes, e.g. gene regulatio},
145 - language = {en},
146 - urldate = {2018-06-12},
147 - journal = {Bioinformatics},
148 - author = {Pan, Xiaoyong and Shen, Hong-Bin and Valencia, Alfonso},
149 - file = {10.1093@bioinformatics@bty364.pdf:/nhome/siniac/lbecquey/Zotero/storage/KUQZ2HNN/10.1093@bioinformatics@bty364.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/TLQUYHEU/4990826.html:text/html}
150 -}
151 -
152 -@article{yi_brief_2017,
153 - title = {A {Brief} {Review} of {RNA}–{Protein} {Interaction} {Database} {Resources}},
154 - volume = {3},
155 - issn = {2311-553X},
156 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832006/},
157 - doi = {10.3390/ncrna3010006},
158 - abstract = {RNA–Protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA–Protein interactions and binding sites from experiments and predictions, RNA–Protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA–Protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA–Protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA–Protein interactions.},
159 - number = {1},
160 - urldate = {2018-06-08},
161 - journal = {Non-Coding RNA},
162 - author = {Yi, Ying and Zhao, Yue and Huang, Yan and Wang, Dong},
163 - month = jan,
164 - year = {2017},
165 - pmid = {29657278},
166 - pmcid = {PMC5832006},
167 - file = {PubMed Central Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/C3ZRG7MJ/Yi et al. - 2017 - A Brief Review of RNA–Protein Interaction Database.pdf:application/pdf}
168 -}
169 -
170 -@article{das_automated_2007,
171 - title = {Automated de novo prediction of native-like {RNA} tertiary structures},
172 - volume = {104},
173 - copyright = {© 2007 by The National Academy of Sciences of the USA. Freely available online through the PNAS open access option.},
174 - issn = {0027-8424, 1091-6490},
175 - url = {http://www.pnas.org/content/104/37/14664},
176 - doi = {10.1073/pnas.0703836104},
177 - abstract = {RNA tertiary structure prediction has been based almost entirely on base-pairing constraints derived from phylogenetic covariation analysis. We describe here a complementary approach, inspired by the Rosetta low-resolution protein structure prediction method, that seeks the lowest energy tertiary structure for a given RNA sequence without using evolutionary information. In a benchmark test of 20 RNA sequences with known structure and lengths of ≈30 nt, the new method reproduces better than 90\% of Watson–Crick base pairs, comparable with the accuracy of secondary structure prediction methods. In more than half the cases, at least one of the top five models agrees with the native structure to better than 4 Å rmsd over the backbone. Most importantly, the method recapitulates more than one-third of non-Watson–Crick base pairs seen in the native structures. Tandem stacks of “sheared” base pairs, base triplets, and pseudoknots are among the noncanonical features reproduced in the models. In the cases in which none of the top five models were native-like, higher energy conformations similar to the native structures are still sampled frequently but not assigned low energies. These results suggest that modest improvements in the energy function, together with the incorporation of information from phylogenetic covariance, may allow confident and accurate structure prediction for larger and more complex RNA chains.},
178 - language = {en},
179 - number = {37},
180 - urldate = {2018-06-04},
181 - journal = {Proceedings of the National Academy of Sciences},
182 - author = {Das, Rhiju and Baker, David},
183 - month = sep,
184 - year = {2007},
185 - pmid = {17726102},
186 - keywords = {ab initio, energy-based, fragment assembly, nucleic acid, Rosetta},
187 - pages = {14664--14669},
188 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/H79FEN6P/Das and Baker - 2007 - Automated de novo prediction of native-like RNA te.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/WH7PUGNW/14664.html:text/html}
189 -}
190 -
191 -@article{cao_physics-based_2011,
192 - title = {Physics-based de novo prediction of {RNA} 3D structures},
193 - volume = {115},
194 - issn = {1520-6106},
195 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072456/},
196 - doi = {10.1021/jp112059y},
197 - abstract = {Current experiments on structural determination cannot keep up the pace with the steadily emerging RNA sequences and new functions. This underscores the request for an accurate model for RNA three-dimensional (3D) structural prediction. Although considerable progress has been made in mechanistic studies, accurate prediction for RNA tertiary folding from sequence remains an unsolved problem. The first and most important requirement for the prediction of RNA structure from physical principles is an accurate free energy model. A recently developed three-vector virtual bond-based RNA folding model (“Vfold”) has allowed us to compute the chain entropy and predict folding free energies and structures for RNA secondary structures and simple pseudoknots. Here we develop a free energy-based method to predict larger more complex RNA tertiary folds. The approach is based on a multiscaling strategy: from the nucleotide sequence, we predict the two-dimensional (2D) structures (defined by the base pairs and tertiary contacts); based on the 2D structure, we construct a 3D scaffold; with the 3D scaffold as the initial state, we combine AMBER energy minimization and PDB-based fragment search to predict the all-atom structure. A key advantage of the approach is the statistical mechanical calculation for the conformational entropy of RNA structures, including those with cross-linked loops. Benchmark tests show that the model leads to significant improvements in RNA 3D structure prediction.},
198 - number = {14},
199 - urldate = {2018-06-04},
200 - journal = {The journal of physical chemistry. B},
201 - author = {Cao, Song and Chen, Shi-Jie},
202 - month = apr,
203 - year = {2011},
204 - pmid = {21413701},
205 - pmcid = {PMC3072456},
206 - pages = {4216--4226},
207 - file = {PubMed Central Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/ZY98QT5K/Cao and Chen - 2011 - Physics-based de novo prediction of RNA 3D structu.pdf:application/pdf}
208 -}
209 -
210 -@article{bottaro_towards_2015,
211 - title = {Towards de novo {RNA} 3D {Structure} {Prediction}},
212 - volume = {2},
213 - copyright = {Copyright (c) 2015 Sandro Bottaro, Francesco Di Palma, Giovanni Bussi},
214 - issn = {2375-2467},
215 - url = {http://www.smartscitech.com/index.php/RD/article/view/544},
216 - doi = {10.14800/rd.544},
217 - abstract = {RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction.},
218 - language = {en},
219 - number = {2},
220 - urldate = {2018-06-04},
221 - journal = {RNA \& DISEASE},
222 - author = {Bottaro, Sandro and Palma, Francesco Di and Bussi, Giovanni},
223 - month = jan,
224 - year = {2015},
225 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/SWAYZQEV/Bottaro et al. - 2015 - Towards de novo RNA 3D Structure Prediction.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/SQMMYVCU/544.html:text/html}
226 -}
227 -
228 -@article{bindewald_multistrand_2016,
229 - title = {Multistrand {Structure} {Prediction} of {Nucleic} {Acid} {Assemblies} and {Design} of {RNA} {Switches}},
230 - volume = {16},
231 - issn = {1530-6984},
232 - url = {https://doi.org/10.1021/acs.nanolett.5b04651},
233 - doi = {10.1021/acs.nanolett.5b04651},
234 - abstract = {RNA is an attractive material for the creation of molecular logic gates that release programmed functionalities only in the presence of specific molecular interaction partners. Here we present HyperFold, a multistrand RNA/DNA structure prediction approach for predicting nucleic acid complexes that can contain pseudoknots. We show that HyperFold also performs competitively compared to other published folding algorithms. We performed a large variety of RNA/DNA hybrid reassociation experiments for different concentrations, DNA toehold lengths, and G+C content and find that the observed tendencies for reassociation correspond well to computational predictions. Importantly, we apply this method to the design and experimental verification of a two-stranded RNA molecular switch that upon binding to a single-stranded RNA toehold disease-marker trigger mRNA changes its conformation releasing an shRNA-like Dicer substrate structure. To demonstrate the concept, connective tissue growth factor (CTGF) mRNA and enhanced green fluorescent protein (eGFP) mRNA were chosen as trigger and target sequences, respectively. In vitro experiments confirm the formation of an RNA switch and demonstrate that the functional unit is being released when the trigger RNA interacts with the switch toehold. The designed RNA switch is shown to be functional in MDA-MB-231 breast cancer cells. Several other switches were also designed and tested. We conclude that this approach has considerable potential because, in principle, it allows the release of an siRNA designed against a gene that differs from the gene that is utilized as a biomarker for a disease state.},
235 - number = {3},
236 - urldate = {2018-05-31},
237 - journal = {Nano Letters},
238 - author = {Bindewald, Eckart and Afonin, Kirill A. and Viard, Mathias and Zakrevsky, Paul and Kim, Taejin and Shapiro, Bruce A.},
239 - month = mar,
240 - year = {2016},
241 - pages = {1726--1735},
242 - file = {ACS Full Text Snapshot:/nhome/siniac/lbecquey/Zotero/storage/285MME3I/acs.nanolett.html:text/html}
243 -}
244 -
245 -@article{ge_novo_2018,
246 - title = {De novo discovery of structural motifs in {RNA} 3D structures through clustering},
247 - volume = {46},
248 - issn = {0305-1048},
249 - url = {https://academic.oup.com/nar/article/46/9/4783/4925243},
250 - doi = {10.1093/nar/gky139},
251 - abstract = {Abstract. As functional components in three-dimensional (3D) conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular a},
252 - language = {en},
253 - number = {9},
254 - urldate = {2018-05-31},
255 - journal = {Nucleic Acids Research},
256 - author = {Ge, Ping and Islam, Shahidul and Zhong, Cuncong and Zhang, Shaojie},
257 - month = may,
258 - year = {2018},
259 - pages = {4783--4793},
260 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/8YS7LY6E/Ge et al. - 2018 - De novo discovery of structural motifs in RNA 3D s.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/4TLRV8ZT/4925243.html:text/html}
261 -}
262 -
263 -@article{wang_rna_2018,
264 - title = {{RNA} 3-dimensional structural motifs as a critical constraint of viroid {RNA} evolution},
265 - volume = {14},
266 - issn = {1553-7374},
267 - url = {http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006801},
268 - doi = {10.1371/journal.ppat.1006801},
269 - language = {en},
270 - number = {2},
271 - urldate = {2018-05-31},
272 - journal = {PLOS Pathogens},
273 - author = {Wang, Ying and Zirbel, Craig L. and Leontis, Neocles B. and Ding, Biao},
274 - month = feb,
275 - year = {2018},
276 - keywords = {Non-coding RNA sequences, RNA structure, RNA viruses, Sequence motif analysis, Viral evolution, Viral replication, Viral structure, Viroids},
277 - pages = {e1006801},
278 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/M3P6GCA7/Wang et al. - 2018 - RNA 3-dimensional structural motifs as a critical .pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/3YRBKI96/article.html:text/html}
279 -}
280 -
281 -@article{lorenz_viennarna_2011,
282 - title = {{ViennaRNA} {Package} 2.0},
283 - volume = {6},
284 - issn = {1748-7188},
285 - url = {https://doi.org/10.1186/1748-7188-6-26},
286 - doi = {10.1186/1748-7188-6-26},
287 - abstract = {Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.},
288 - urldate = {2018-05-31},
289 - journal = {Algorithms for Molecular Biology},
290 - author = {Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.},
291 - month = nov,
292 - year = {2011},
293 - keywords = {Consensus Structure, Folding Algorithm, Matthews Correlation Coefficient, Minimum Free Energy, Partition Function},
294 - pages = {26},
295 - annote = {Pages 26 in PDF},
296 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/WFPBA2H8/Lorenz et al. - 2011 - ViennaRNA Package 2.0.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/ADNFF9EA/1748-7188-6-26.html:text/html}
297 -}
298 -
299 -@article{janssen_rna_2015,
300 - title = {The {RNA} shapes studio},
301 - volume = {31},
302 - issn = {1367-4803},
303 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308662/},
304 - doi = {10.1093/bioinformatics/btu649},
305 - abstract = {Motivation: Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach., Results: We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss. As a spin-off, we obtain heretofore unavailable functionality: e. g. with pKiss, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool pAliKiss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways., Availability and implementation: As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio., Contact: bibi-help@cebitec.uni-bielefeld.de},
306 - number = {3},
307 - urldate = {2018-05-31},
308 - journal = {Bioinformatics},
309 - author = {Janssen, Stefan and Giegerich, Robert},
310 - month = feb,
311 - year = {2015},
312 - pmid = {25273103},
313 - pmcid = {PMC4308662},
314 - pages = {423--425},
315 - file = {PubMed Central Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/KFQTVDR3/Janssen and Giegerich - 2015 - The RNA shapes studio.pdf:application/pdf}
316 -}
317 -
318 -@article{parlea_rna_2016,
319 - series = {Advances in {RNA} {Structure} {Determination}},
320 - title = {The {RNA} 3D {Motif} {Atlas}: {Computational} methods for extraction, organization and evaluation of {RNA} motifs},
321 - volume = {103},
322 - issn = {1046-2023},
323 - shorttitle = {The {RNA} 3D {Motif} {Atlas}},
324 - url = {http://www.sciencedirect.com/science/article/pii/S1046202316301049},
325 - doi = {10.1016/j.ymeth.2016.04.025},
326 - abstract = {RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction “loops” of their secondary structure representations. As many as 40\% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs.},
327 - urldate = {2018-05-31},
328 - journal = {Methods},
329 - author = {Parlea, Lorena G. and Sweeney, Blake A. and Hosseini-Asanjan, Maryam and Zirbel, Craig L. and Leontis, Neocles B.},
330 - month = jul,
331 - year = {2016},
332 - keywords = {Hairpin loop, Internal loop, Multi-helix junction loop, Non-Watson-Crick basepair, RNA 3D Motif, Structured RNA molecules},
333 - pages = {99--119},
334 - file = {ScienceDirect Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/HM9ZDD83/Parlea et al. - 2016 - The RNA 3D Motif Atlas Computational methods for .pdf:application/pdf;ScienceDirect Snapshot:/nhome/siniac/lbecquey/Zotero/storage/ANJRICVQ/S1046202316301049.html:text/html}
335 -}
336 -
337 -@article{legendre_bi-objective_2018,
338 - title = {Bi-objective integer programming for {RNA} secondary structure prediction with pseudoknots},
339 - volume = {19},
340 - issn = {1471-2105},
341 - url = {https://doi.org/10.1186/s12859-018-2007-7},
342 - doi = {10.1186/s12859-018-2007-7},
343 - abstract = {RNA structure prediction is an important field in bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict. Almost all existing methods are based on a single model and return one solution, often missing the real structure. An alternative approach would be to combine different models and return a (small) set of solutions, maximizing its quality and diversity in order to increase the probability that it contains the real structure.},
344 - urldate = {2018-05-24},
345 - journal = {BMC Bioinformatics},
346 - author = {Legendre, Audrey and Angel, Eric and Tahi, Fariza},
347 - month = jan,
348 - year = {2018},
349 - keywords = {RNA, Bi-objective, Integer programming, Optimal solutions, Pseudoknot, Secondary structure, Sub-optimal solutions},
350 - pages = {13},
351 - annote = {Pages 13 in PDF},
352 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/4YMW5M4S/Legendre et al. - 2018 - Bi-objective integer programming for RNA secondary.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/XP46BMHH/s12859-018-2007-7.html:text/html}
353 -}
354 -
355 -@article{sarver_fr3d:_2008,
356 - title = {{FR}3D: finding local and composite recurrent structural motifs in {RNA} 3D structures},
357 - volume = {56},
358 - issn = {1432-1416},
359 - shorttitle = {{FR}3D},
360 - url = {https://doi.org/10.1007/s00285-007-0110-x},
361 - doi = {10.1007/s00285-007-0110-x},
362 - abstract = {New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes.},
363 - language = {en},
364 - number = {1},
365 - urldate = {2018-10-10},
366 - journal = {Journal of Mathematical Biology},
367 - author = {Sarver, Michael and Zirbel, Craig L. and Stombaugh, Jesse and Mokdad, Ali and Leontis, Neocles B.},
368 - month = jan,
369 - year = {2008},
370 - keywords = {05C85, 92C40},
371 - pages = {215--252}
372 -}
373 -
374 -@article{petrov_webfr3dserver_2011,
375 - title = {{WebFR}3D—a server for finding, aligning and analyzing recurrent {RNA} 3D motifs},
376 - volume = {39},
377 - issn = {0305-1048},
378 - url = {https://academic.oup.com/nar/article/39/suppl_2/W50/2505799},
379 - doi = {10.1093/nar/gkr249},
380 - abstract = {Abstract. WebFR3D is the on-line version of ‘Find RNA 3D’ (FR3D), a program for annotating atomic-resolution RNA 3D structure files and searching them efficie},
381 - language = {en},
382 - number = {suppl\_2},
383 - urldate = {2018-10-10},
384 - journal = {Nucleic Acids Research},
385 - author = {Petrov, Anton I. and Zirbel, Craig L. and Leontis, Neocles B.},
386 - month = jul,
387 - year = {2011},
388 - pages = {W50--W55},
389 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/WVGVFLFH/Petrov et al. - 2011 - WebFR3D—a server for finding, aligning and analyzi.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/8NMZZLKV/2505799.html:text/html}
390 -}
391 -
392 -@article{petrov_automated_2013,
393 - title = {Automated classification of {RNA} 3D motifs and the {RNA} 3D {Motif} {Atlas}},
394 - volume = {19},
395 - issn = {1355-8382, 1469-9001},
396 - url = {http://rnajournal.cshlp.org/content/19/10/1327},
397 - doi = {10.1261/rna.039438.113},
398 - abstract = {A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms},
399 - language = {en},
400 - number = {10},
401 - urldate = {2018-10-10},
402 - journal = {RNA},
403 - author = {Petrov, Anton I. and Zirbel, Craig L. and Leontis, Neocles B.},
404 - month = jan,
405 - year = {2013},
406 - pmid = {23970545},
407 - pages = {1327--1340},
408 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/GIC5F2CJ/Petrov et al. - 2013 - Automated classification of RNA 3D motifs and the .pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/UJFVEML3/1327.full.html:text/html}
409 -}
410 -
411 -@article{lu_dssr:_2015,
412 - title = {{DSSR}: an integrated software tool for dissecting the spatial structure of {RNA}},
413 - volume = {43},
414 - issn = {0305-1048},
415 - shorttitle = {{DSSR}},
416 - url = {https://academic.oup.com/nar/article/43/21/e142/2468098},
417 - doi = {10.1093/nar/gkv716},
418 - abstract = {Abstract. Insight into the three-dimensional architecture of RNA is essential for understanding its cellular functions. However, even the classic transfer RNA},
419 - language = {en},
420 - number = {21},
421 - urldate = {2018-10-09},
422 - journal = {Nucleic Acids Research},
423 - author = {Lu, Xiang-Jun and Bussemaker, Harmen J. and Olson, Wilma K.},
424 - month = dec,
425 - year = {2015},
426 - pages = {e142--e142},
427 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/NURMS9UY/Lu et al. - 2015 - DSSR an integrated software tool for dissecting t.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/BTZXBR6S/2468098.html:text/html}
428 -}
429 -
430 -@article{antczak_rnapdbeewebserver_2014,
431 - title = {{RNApdbee}—a webserver to derive secondary structures from pdb files of knotted and unknotted {RNAs}},
432 - volume = {42},
433 - issn = {0305-1048},
434 - url = {https://academic.oup.com/nar/article/42/W1/W368/2435287},
435 - doi = {10.1093/nar/gku330},
436 - abstract = {Abstract. In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. Thi},
437 - language = {en},
438 - number = {W1},
439 - urldate = {2018-10-09},
440 - journal = {Nucleic Acids Research},
441 - author = {Antczak, Maciej and Zok, Tomasz and Popenda, Mariusz and Lukasiak, Piotr and Adamiak, Ryszard W. and Blazewicz, Jacek and Szachniuk, Marta},
442 - month = jul,
443 - year = {2014},
444 - pages = {W368--W372},
445 - file = {Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/RWXNJQH6/Antczak et al. - 2014 - RNApdbee—a webserver to derive secondary structure.pdf:application/pdf;Snapshot:/nhome/siniac/lbecquey/Zotero/storage/H6CZVH4F/2435287.html:text/html}
446 -}
447 -
448 -
449 -@article{dirksAlgorithmComputingNucleic2004,
450 - title = {An Algorithm for Computing Nucleic Acid Base-Pairing Probabilities Including Pseudoknots},
451 - volume = {25},
452 - copyright = {Copyright \textcopyright{} 2004 Wiley Periodicals, Inc.},
453 - issn = {1096-987X},
454 - doi = {10.1002/jcc.20057},
455 - abstract = {Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. \textcopyright{} 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295\textendash{}1304, 2004},
456 - language = {en},
457 - number = {10},
458 - journal = {Journal of Computational Chemistry},
459 - author = {Dirks, Robert M. and Pierce, Niles A.},
460 - year = {2004},
461 - keywords = {pseudoknots,RNA,DNA,base-pairing probabilities,partition function},
462 - pages = {1295-1304},
463 - file = {/nhome/siniac/lbecquey/Zotero/storage/LA8RHBVN/jcc.html}
464 -}
465 -
466 -
467 -@article{laing_computational_2010,
468 - title = {Computational approaches to 3D modeling of {RNA}},
469 - volume = {22},
470 - issn = {0953-8984},
471 - url = {http://stacks.iop.org/0953-8984/22/i=28/a=283101},
472 - doi = {10.1088/0953-8984/22/28/283101},
473 - abstract = {Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research.},
474 - language = {en},
475 - number = {28},
476 - urldate = {2018-10-09},
477 - journal = {Journal of Physics: Condensed Matter},
478 - author = {Laing, Christian and Schlick, Tamar},
479 - year = {2010},
480 - pages = {283101}
481 -}
482 -
483 -@article{dawson_computational_2016,
484 - series = {Theory and simulation • {Macromolcular} machines},
485 - title = {Computational modeling of {RNA} 3D structures and interactions},
486 - volume = {37},
487 - issn = {0959-440X},
488 - url = {http://www.sciencedirect.com/science/article/pii/S0959440X15001700},
489 - doi = {10.1016/j.sbi.2015.11.007},
490 - abstract = {RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.},
491 - urldate = {2018-10-09},
492 - journal = {Current Opinion in Structural Biology},
493 - author = {Dawson, Wayne K and Bujnicki, Janusz M},
494 - month = apr,
495 - year = {2016},
496 - pages = {22--28},
497 - file = {ScienceDirect Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/7V5SQ8PN/Dawson et Bujnicki - 2016 - Computational modeling of RNA 3D structures and in.pdf:application/pdf;ScienceDirect Snapshot:/nhome/siniac/lbecquey/Zotero/storage/CDMTYU7W/S0959440X15001700.html:text/html}
498 -}
499 -
500 -@article{laing_computational_2011,
501 - title = {Computational approaches to {RNA} structure prediction, analysis, and design},
502 - volume = {21},
503 - issn = {0959-440X},
504 - url = {http://www.sciencedirect.com/science/article/pii/S0959440X11000674},
505 - doi = {10.1016/j.sbi.2011.03.015},
506 - abstract = {RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires RNA tertiary structure knowledge. Although modeling approaches for the study of RNA structures and dynamics lag behind efforts in protein folding, much progress has been achieved in the past two years. Here, we review recent advances in RNA folding algorithms, RNA tertiary motif discovery, applications of graph theory approaches to RNA structure and function, and in silico generation of RNA sequence pools for aptamer design. Advances within each area can be combined to impact many problems in RNA structure and function.},
507 - number = {3},
508 - urldate = {2018-10-09},
509 - journal = {Current Opinion in Structural Biology},
510 - author = {Laing, Christian and Schlick, Tamar},
511 - month = jun,
512 - year = {2011},
513 - pages = {306--318},
514 - file = {ScienceDirect Snapshot:/nhome/siniac/lbecquey/Zotero/storage/LWS5RU5Z/S0959440X11000674.html:text/html}
515 -}
516 -
517 -
518 -@article{reinharz2018mining,
519 - title={Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families},
520 - author={Reinharz, Vladimir and Soul{\'e}, Antoine and Westhof, Eric and Waldisp{\"u}hl, J{\'e}r{\^o}me and Denise, Alain},
521 - journal={Nucleic Acids Research},
522 - volume={46},
523 - number={8},
524 - pages={3841--3851},
525 - year={2018},
526 - publisher={Oxford University Press}
527 -}
528 -
529 -@article{sato_ipknot:_2011,
530 - title = {{IPknot}: fast and accurate prediction of {RNA} secondary structures with pseudoknots using integer programming},
531 - volume = {27},
532 - issn = {1367-4803},
533 - shorttitle = {{IPknot}},
534 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117384/},
535 - doi = {10.1093/bioinformatics/btr215},
536 - abstract = {Motivation: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy., Results: We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. The problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods., Availability: The program of IPknot is available at http://www.ncrna.org/software/ipknot/. IPknot is also available as a web server at http://rna.naist.jp/ipknot/., Contact: satoken@k.u-tokyo.ac.jp; ykato@is.naist.jp, Supplementary information: Supplementary data are available at Bioinformatics online.},
537 - number = {13},
538 - urldate = {2018-10-12},
539 - journal = {Bioinformatics},
540 - author = {Sato, Kengo and Kato, Yuki and Hamada, Michiaki and Akutsu, Tatsuya and Asai, Kiyoshi},
541 - month = jul,
542 - year = {2011},
543 - pmid = {21685106},
544 - pmcid = {PMC3117384},
545 - pages = {i85--i93},
546 - file = {Texte intégral:/nhome/siniac/lbecquey/Zotero/storage/EEWT77EA/Sato et al. - 2011 - IPknot fast and accurate prediction of RNA second.pdf:application/pdf}
547 -}
548 -
549 -
550 -@article{zirbel_identifying_2015,
551 - title = {Identifying novel sequence variants of {RNA} 3D motifs},
552 - volume = {43},
553 - issn = {0305-1048},
554 - url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551918/},
555 - doi = {10.1093/nar/gkv651},
556 - abstract = {Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download.},
557 - number = {15},
558 - urldate = {2018-10-19},
559 - journal = {Nucleic Acids Research},
560 - author = {Zirbel, Craig L. and Roll, James and Sweeney, Blake A. and Petrov, Anton I. and Pirrung, Meg and Leontis, Neocles B.},
561 - month = sep,
562 - year = {2015},
563 - pmid = {26130723},
564 - pmcid = {PMC4551918},
565 - pages = {7504--7520},
566 - file = {PubMed Central Full Text PDF:/nhome/siniac/lbecquey/Zotero/storage/C68JKL5J/Zirbel et al. - 2015 - Identifying novel sequence variants of RNA 3D moti.pdf:application/pdf}
567 -}
568 -
569 -
570 -@software{cplex,
571 - author = {IBM ILOG},
572 - title = {{CPLEX}: {CPLEX} {Optimizer} (Academic license)},
573 - version = {12.8},
574 - howpublished = {\url{https://www.ibm.com/analytics/optimization-modeling-interfaces}},
575 - year = {2018}
576 -}
577 -
578 -@article{andronescu2008rna,
579 - title={RNA STRAND: the RNA secondary structure and statistical analysis database},
580 - author={Andronescu, Mirela and Bereg, Vera and Hoos, Holger H and Condon, Anne},
581 - journal={BMC bioinformatics},
582 - volume={9},
583 - number={1},
584 - pages={340},
585 - year={2008},
586 - publisher={BioMed Central}
587 -}
...\ No newline at end of file ...\ No newline at end of file
...@@ -15,15 +15,15 @@ import ast ...@@ -15,15 +15,15 @@ import ast
15 15
16 # Retrieve Paths from file EditMe 16 # Retrieve Paths from file EditMe
17 jar3dexec = "" 17 jar3dexec = ""
18 -HLmotifDir = ""
19 -ILmotifDir = ""
20 -descfolder = ""
21 bypdir = "" 18 bypdir = ""
22 biorseoDir = "." 19 biorseoDir = "."
23 exec(compile(open(biorseoDir+"/EditMe").read(), '', 'exec')) 20 exec(compile(open(biorseoDir+"/EditMe").read(), '', 'exec'))
24 runDir = path.dirname(path.realpath(__file__)) 21 runDir = path.dirname(path.realpath(__file__))
25 dataFile = argv[1] 22 dataFile = argv[1]
26 outputDir = biorseoDir + "/results/" 23 outputDir = biorseoDir + "/results/"
24 +HLmotifDir = biorseoDir + "/data/modules/BGSU/HL/3.2/lib"
25 +ILmotifDir = biorseoDir + "/data/modules/BGSU/IL/3.2/lib"
26 +descfolder = biorseoDir + "/data/modules/DESC"
27 27
28 # Create some folders to store the results 28 # Create some folders to store the results
29 subprocess.call(["mkdir", "-p", outputDir]) 29 subprocess.call(["mkdir", "-p", outputDir])
...@@ -360,8 +360,8 @@ def launch_RNAMoIP(seq_, header_, basename): ...@@ -360,8 +360,8 @@ def launch_RNAMoIP(seq_, header_, basename):
360 ninsertions = [ t[1] for t in results if t[0] != ""] 360 ninsertions = [ t[1] for t in results if t[0] != ""]
361 scores = [ t[2] for t in results if t[0] != ""] 361 scores = [ t[2] for t in results if t[0] != ""]
362 rna = open(outputDir + basename + ".moip", "w") 362 rna = open(outputDir + basename + ".moip", "w")
363 - rna.write(header_) 363 + rna.write(header_+'\n')
364 - rna.write(seq_) 364 + rna.write(seq_+'\n')
365 for p,n,s in zip(predictions, ninsertions, scores): 365 for p,n,s in zip(predictions, ninsertions, scores):
366 rna.write(p+'\t'+str(n)+'\t'+str(s)+'\n') 366 rna.write(p+'\t'+str(n)+'\t'+str(s)+'\n')
367 rna.close() 367 rna.close()
...@@ -885,8 +885,8 @@ class RNA: ...@@ -885,8 +885,8 @@ class RNA:
885 if ss not in self.biorseoBGSUBayesPairA.predictions: 885 if ss not in self.biorseoBGSUBayesPairA.predictions:
886 self.biorseoBGSUBayesPairA.predictions.append(ss) 886 self.biorseoBGSUBayesPairA.predictions.append(ss)
887 self.biorseoBGSUBayesPairA.ninsertions.append(lines[i].count('+')) 887 self.biorseoBGSUBayesPairA.ninsertions.append(lines[i].count('+'))
888 - else: 888 + # else:
889 - print(targetdir+ self.basename + ".bgsubypA not found !") 889 + # print(targetdir+ self.basename + ".bgsubypA not found !")
890 890
891 def get_biorseoBGSUBayesPairB_results(self, targetdir): 891 def get_biorseoBGSUBayesPairB_results(self, targetdir):
892 if path.isfile(targetdir+ self.basename + ".bgsubypB"): 892 if path.isfile(targetdir+ self.basename + ".bgsubypB"):
...@@ -898,8 +898,8 @@ class RNA: ...@@ -898,8 +898,8 @@ class RNA:
898 if ss not in self.biorseoBGSUBayesPairB.predictions: 898 if ss not in self.biorseoBGSUBayesPairB.predictions:
899 self.biorseoBGSUBayesPairB.predictions.append(ss) 899 self.biorseoBGSUBayesPairB.predictions.append(ss)
900 self.biorseoBGSUBayesPairB.ninsertions.append(lines[i].count('+')) 900 self.biorseoBGSUBayesPairB.ninsertions.append(lines[i].count('+'))
901 - else: 901 + # else:
902 - print(targetdir+ self.basename + ".bgsubypB not found !") 902 + # print(targetdir+ self.basename + ".bgsubypB not found !")
903 903
904 def get_biorseoBGSUBayesPairC_results(self, targetdir): 904 def get_biorseoBGSUBayesPairC_results(self, targetdir):
905 if path.isfile(targetdir+ self.basename + ".bgsubypC"): 905 if path.isfile(targetdir+ self.basename + ".bgsubypC"):
...@@ -911,8 +911,8 @@ class RNA: ...@@ -911,8 +911,8 @@ class RNA:
911 if ss not in self.biorseoBGSUBayesPairC.predictions: 911 if ss not in self.biorseoBGSUBayesPairC.predictions:
912 self.biorseoBGSUBayesPairC.predictions.append(ss) 912 self.biorseoBGSUBayesPairC.predictions.append(ss)
913 self.biorseoBGSUBayesPairC.ninsertions.append(lines[i].count('+')) 913 self.biorseoBGSUBayesPairC.ninsertions.append(lines[i].count('+'))
914 - else: 914 + # else:
915 - print(targetdir+ self.basename + ".bgsubypC not found !") 915 + # print(targetdir+ self.basename + ".bgsubypC not found !")
916 916
917 def get_biorseoBGSUBayesPairD_results(self, targetdir): 917 def get_biorseoBGSUBayesPairD_results(self, targetdir):
918 if path.isfile(targetdir+ self.basename + ".bgsubypD"): 918 if path.isfile(targetdir+ self.basename + ".bgsubypD"):
...@@ -924,8 +924,8 @@ class RNA: ...@@ -924,8 +924,8 @@ class RNA:
924 if ss not in self.biorseoBGSUBayesPairD.predictions: 924 if ss not in self.biorseoBGSUBayesPairD.predictions:
925 self.biorseoBGSUBayesPairD.predictions.append(ss) 925 self.biorseoBGSUBayesPairD.predictions.append(ss)
926 self.biorseoBGSUBayesPairD.ninsertions.append(lines[i].count('+')) 926 self.biorseoBGSUBayesPairD.ninsertions.append(lines[i].count('+'))
927 - else: 927 + # else:
928 - print(targetdir+ self.basename + ".bgsubypD not found !") 928 + # print(targetdir+ self.basename + ".bgsubypD not found !")
929 929
930 def load_results_from(self, targetDir): 930 def load_results_from(self, targetDir):
931 self.get_biokop_results() 931 self.get_biokop_results()
...@@ -1003,9 +1003,9 @@ for nt, number in ignored_nt_dict.items(): ...@@ -1003,9 +1003,9 @@ for nt, number in ignored_nt_dict.items():
1003 tot = len(RNAcontainer) 1003 tot = len(RNAcontainer)
1004 print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudoknots." % (tot, pk_counter)) 1004 print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudoknots." % (tot, pk_counter))
1005 1005
1006 -# # ================= PREDICTION OF STRUCTURES =============================== 1006 +# #================= PREDICTION OF STRUCTURES ===============================
1007 1007
1008 -# # define job list 1008 +# #define job list
1009 # joblist = [] 1009 # joblist = []
1010 # for instance in RNAcontainer: 1010 # for instance in RNAcontainer:
1011 # basename = instance.basename 1011 # basename = instance.basename
...@@ -1017,7 +1017,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1017,7 +1017,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1017 # # BayesPairing and BGSUBayesPairing 1017 # # BayesPairing and BGSUBayesPairing
1018 # joblist.append(Job(function=launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BayesPairing, checkArgs=[basename])) 1018 # joblist.append(Job(function=launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BayesPairing, checkArgs=[basename]))
1019 # joblist.append(Job(function=launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BGSUBayesPairing, checkArgs=[basename])) 1019 # joblist.append(Job(function=launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BGSUBayesPairing, checkArgs=[basename]))
1020 -# # bmotinBGSUJAR3DA-D 1020 +# # biorseoBGSUJAR3DA-D
1021 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, False])) 1021 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, False]))
1022 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, False])) 1022 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, False]))
1023 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, False])) 1023 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, False]))
...@@ -1026,7 +1026,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1026,7 +1026,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1026 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, True])) 1026 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, True]))
1027 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, True])) 1027 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, True]))
1028 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, True])) 1028 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, True]))
1029 -# # bmotinBGSUBayesPairA-D 1029 +# # biorseoBGSUBayesPairA-D
1030 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, False])) 1030 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, False]))
1031 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, False])) 1031 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, False]))
1032 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, False])) 1032 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, False]))
...@@ -1035,7 +1035,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1035,7 +1035,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1035 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, True])) 1035 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, True]))
1036 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, True])) 1036 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, True]))
1037 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, True])) 1037 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, True]))
1038 -# # bmotinBayesPairA-D 1038 +# # biorseoBayesPairA-D
1039 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, False])) 1039 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, False]))
1040 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, False])) 1040 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, False]))
1041 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, False])) 1041 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, False]))
...@@ -1049,7 +1049,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1049,7 +1049,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1049 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, False])) 1049 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"noPK/" + basename + ".rawB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, False]))
1050 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, True])) 1050 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawA", "--type", "A"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawA, checkArgs=[basename, True]))
1051 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, True])) 1051 # joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir + basename + ".fa", "-d", descfolder, "-o", outputDir+"PK/" + basename + ".rawB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoRawB, checkArgs=[basename, True]))
1052 -# # RNA MoIP 1052 +# # RNA-MoIP
1053 # joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename])) 1053 # joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename]))
1054 # # Biokop 1054 # # Biokop
1055 # joblist.append(Job(command=[biorseoDir + "/../biokop/biokop", "-n1", "-i", outputDir + basename + ".fa", "-o", outputDir + basename + ".biok"], priority=5, timeout=15000, how_many_in_parallel=3, checkFunc=check_biokop, checkArgs=[basename])) 1055 # joblist.append(Job(command=[biorseoDir + "/../biokop/biokop", "-n1", "-i", outputDir + basename + ".fa", "-o", outputDir + basename + ".biok"], priority=5, timeout=15000, how_many_in_parallel=3, checkFunc=check_biokop, checkArgs=[basename]))
...@@ -1088,13 +1088,15 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno ...@@ -1088,13 +1088,15 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
1088 # print() 1088 # print()
1089 # for j in fails: 1089 # for j in fails:
1090 # print(j.cmd_) 1090 # print(j.cmd_)
1091 - 1091 +# else:
1092 -# exit() 1092 +# print()
1093 - 1093 +# print("Computations ran successfully.")
1094 +# print()
1094 1095
1095 1096
1096 # ================= Statistics (without pseudoknots) ======================== 1097 # ================= Statistics (without pseudoknots) ========================
1097 1098
1099 +print("Loading results from files... (without pseudoknots)")
1098 # load results in objects 1100 # load results in objects
1099 for instance in RNAcontainer: 1101 for instance in RNAcontainer:
1100 instance.load_results_from(outputDir + "noPK/") 1102 instance.load_results_from(outputDir + "noPK/")
...@@ -1145,7 +1147,7 @@ x_noPK_fully = [ ...@@ -1145,7 +1147,7 @@ x_noPK_fully = [
1145 print() 1147 print()
1146 print("Without PK:") 1148 print("Without PK:")
1147 print("%s RNAsubopt predictions" % is_all(len(x_noPK[0]), tot)) 1149 print("%s RNAsubopt predictions" % is_all(len(x_noPK[0]), tot))
1148 -print("%s RNA MoIP predictions" % is_all(len(x_noPK[1]), tot)) 1150 +print("%s RNA-MoIP predictions" % is_all(len(x_noPK[1]), tot))
1149 print("%s biorseo + BGSU + JAR3D + f1A predictions" % is_all(len(x_noPK[2]), tot)) 1151 print("%s biorseo + BGSU + JAR3D + f1A predictions" % is_all(len(x_noPK[2]), tot))
1150 print("%s biorseo + BGSU + JAR3D + f1B predictions" % is_all(len(x_noPK[3]), tot)) 1152 print("%s biorseo + BGSU + JAR3D + f1B predictions" % is_all(len(x_noPK[3]), tot))
1151 print("%s biorseo + BGSU + JAR3D + f1C predictions" % is_all(len(x_noPK[4]), tot)) 1153 print("%s biorseo + BGSU + JAR3D + f1C predictions" % is_all(len(x_noPK[4]), tot))
...@@ -1174,6 +1176,7 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of RNA-Mo ...@@ -1174,6 +1176,7 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of RNA-Mo
1174 1176
1175 # ================= Statistics (with pseudoknots) ======================== 1177 # ================= Statistics (with pseudoknots) ========================
1176 1178
1179 +print("Loading results from files... (with pseudoknots)")
1177 # load results in objects 1180 # load results in objects
1178 for instance in RNAcontainer: 1181 for instance in RNAcontainer:
1179 instance.load_results_from(outputDir + "PK/") 1182 instance.load_results_from(outputDir + "PK/")
...@@ -1271,8 +1274,8 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop ...@@ -1271,8 +1274,8 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop
1271 # print("RNA-MOIP",":",x_noPK[1]) 1274 # print("RNA-MOIP",":",x_noPK[1])
1272 # for data, name in zip(x_PK, labels): 1275 # for data, name in zip(x_PK, labels):
1273 # print(name,":",data) 1276 # print(name,":",data)
1274 -# labels = ["RNAsubopt","Biokop\t", "RNA MoIP\t","RawA\t","RawB\t","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA\t","JAR3DB\t","JAR3DC\t","JAR3DD\t","BGSUBPairingA","BGSUBPairingB","BGSUBPairingC","BGSUBPairingD"] 1277 +# labels = ["RNAsubopt","Biokop\t", "RNA-MoIP\t","RawA\t","RawB\t","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA\t","JAR3DB\t","JAR3DC\t","JAR3DD\t","BGSUBPairingA","BGSUBPairingB","BGSUBPairingC","BGSUBPairingD"]
1275 -# # for r in RNAcontainer: 1278 +# for r in RNAcontainer:
1276 # print("\n",r.header_,"\nTrue structure:\t", r.true2d) 1279 # print("\n",r.header_,"\nTrue structure:\t", r.true2d)
1277 # for m, name in zip([r.rnasubopt, r.biokop, r.rnamoip, 1280 # for m, name in zip([r.rnasubopt, r.biokop, r.rnamoip,
1278 # r.biorseoRawA, 1281 # r.biorseoRawA,
...@@ -1295,7 +1298,7 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop ...@@ -1295,7 +1298,7 @@ print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop
1295 1298
1296 merge = [ x_PK_fully[0], # Biokop 1299 merge = [ x_PK_fully[0], # Biokop
1297 x_noPK_fully[0], # RNA subopt 1300 x_noPK_fully[0], # RNA subopt
1298 - x_noPK_fully[1], # RNA MoIP 1301 + x_noPK_fully[1], # RNA-MoIP
1299 x_noPK_fully[2], x_PK_fully[2], #biorseoRawA 1302 x_noPK_fully[2], x_PK_fully[2], #biorseoRawA
1300 x_noPK_fully[3], x_PK_fully[3], #biorseoRawB 1303 x_noPK_fully[3], x_PK_fully[3], #biorseoRawB
1301 x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA 1304 x_noPK_fully[4], x_PK_fully[4], #biorseoBayesPairA
...@@ -1329,7 +1332,7 @@ colors = [ 'green', 'blue', 'goldenrod', ...@@ -1329,7 +1332,7 @@ colors = [ 'green', 'blue', 'goldenrod',
1329 'lime', 'lime' 1332 'lime', 'lime'
1330 ] 1333 ]
1331 labels = [ "Biokop", "RNAsubopt", 1334 labels = [ "Biokop", "RNAsubopt",
1332 - "RNA MoIP", 1335 + "RNA-MoIP",
1333 "$f_{1A}$", 1336 "$f_{1A}$",
1334 "$f_{1B}$", 1337 "$f_{1B}$",
1335 "$f_{1A}$", 1338 "$f_{1A}$",
...@@ -1360,7 +1363,7 @@ for patch, color in zip(bplot['boxes'], colors): ...@@ -1360,7 +1363,7 @@ for patch, color in zip(bplot['boxes'], colors):
1360 # plt.axhline(y=0, color="black", linewidth=1) 1363 # plt.axhline(y=0, color="black", linewidth=1)
1361 # plt.axhline(y=1, color="black", linewidth=1) 1364 # plt.axhline(y=1, color="black", linewidth=1)
1362 plt.xticks([1.0+i for i in range(16)], labels[1:]) 1365 plt.xticks([1.0+i for i in range(16)], labels[1:])
1363 -plt.ylim((0, 1.01)) 1366 +plt.ylim((0.5, 1.01))
1364 plt.ylabel("MCC", fontsize=12) 1367 plt.ylabel("MCC", fontsize=12)
1365 plt.subplots_adjust(left=0.05, right=0.95) 1368 plt.subplots_adjust(left=0.05, right=0.95)
1366 # plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0])) 1369 # plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
...@@ -1382,7 +1385,7 @@ for patch, color in zip(bplot['boxes'], colors): ...@@ -1382,7 +1385,7 @@ for patch, color in zip(bplot['boxes'], colors):
1382 # plt.axhline(y=0, color="black", linewidth=1) 1385 # plt.axhline(y=0, color="black", linewidth=1)
1383 # plt.axhline(y=1, color="black", linewidth=1) 1386 # plt.axhline(y=1, color="black", linewidth=1)
1384 plt.xticks([1.0+i for i in range(16)], labels) 1387 plt.xticks([1.0+i for i in range(16)], labels)
1385 -plt.ylim((0, 1.01)) 1388 +plt.ylim((0.5, 1.01))
1386 plt.ylabel("MCC", fontsize=12) 1389 plt.ylabel("MCC", fontsize=12)
1387 plt.subplots_adjust(left=0.05, right=0.95) 1390 plt.subplots_adjust(left=0.05, right=0.95)
1388 # plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12) 1391 # plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
...@@ -1392,20 +1395,18 @@ plt.show() ...@@ -1392,20 +1395,18 @@ plt.show()
1392 1395
1393 1396
1394 # # ================== MCC performance ==================================== 1397 # # ================== MCC performance ====================================
1395 -# # plt.subplot(141) 1398 +# RNAcontainer.sort(key=lambda x: x.rnasubopt.max_mcc)
1396 -
1397 -# RNAs_fully_predicted.sort(key=lambda x: x.rnasubopt.max_mcc)
1398 1399
1399 # x = [ 1400 # x = [
1400 -# [ rna.rnasubopt.max_mcc for rna in RNAs_fully_predicted], 1401 +# [ rna.rnasubopt.max_mcc for rna in RNAcontainer],
1401 -# [ rna.rnamoip.max_mcc for rna in RNAs_fully_predicted], 1402 +# [ rna.rnamoip.max_mcc for rna in RNAcontainer],
1402 -# #[ rna.biorseoRawA.max_mcc for rna in RNAs_fully_predicted], 1403 +# # [ rna.biorseoRawA.max_mcc for rna in RNAs_fully_predicted],
1403 # # [ rna.biorseoRawB.max_mcc for rna in RNAs_fully_predicted], 1404 # # [ rna.biorseoRawB.max_mcc for rna in RNAs_fully_predicted],
1404 -# #[ rna.biokop.max_mcc for rna in RNAs_fully_predicted], 1405 +# # [ rna.biokop.max_mcc for rna in RNAs_fully_predicted],
1405 -# #[ rna.biorseoBGSUJAR3DA.max_mcc for rna in RNAs_fully_predicted] 1406 +# # [ rna.biorseoBGSUJAR3DA.max_mcc for rna in RNAs_fully_predicted]
1406 # ] 1407 # ]
1407 -# colors = ['xkcd:blue','goldenrod']#, 'green', 'cyan'] 1408 +# colors = ['xkcd:blue','goldenrod']#xkcd:red', 'green', 'cyan']
1408 -# labels = ["Best RNAsubopt MCC", "Best RNA-MoIP MCC"]#, "Best Biokop prediction", "Best JAR3DA prediction"] 1409 +# labels = ["Best RNAsubopt MCC", "Best RNA-MoIP MCC"]# "Best RawA prediction", "Best Biokop prediction", "Best JAR3DA prediction"]
1409 # for y, col, lab in zip(x, colors, labels): 1410 # for y, col, lab in zip(x, colors, labels):
1410 # x_data = [ i for i in range(len(y)) if y[i]] 1411 # x_data = [ i for i in range(len(y)) if y[i]]
1411 # y_data = [ i for i in y if i] 1412 # y_data = [ i for i in y if i]
...@@ -1544,7 +1545,7 @@ plt.show() ...@@ -1544,7 +1545,7 @@ plt.show()
1544 # [ rna.biokop.max_mcc - rna.rnasubopt.max_mcc for rna in RNAcontainer if len(rna.biokop.predictions)], 1545 # [ rna.biokop.max_mcc - rna.rnasubopt.max_mcc for rna in RNAcontainer if len(rna.biokop.predictions)],
1545 #] 1546 #]
1546 # colors = ['xkcd:goldenrod', 'xkcd:red', 'firebrick', 'limegreen'] 1547 # colors = ['xkcd:goldenrod', 'xkcd:red', 'firebrick', 'limegreen']
1547 -# labels = ["$\Delta$MCC(RNAsubopt,RNA MoIP)","$\Delta$MCC(RNAsubopt,RNA MoBOIP)", 1548 +# labels = ["$\Delta$MCC(RNAsubopt,RNA-MoIP)","$\Delta$MCC(RNAsubopt,RNA MoBOIP)",
1548 # "$\Delta$MCC(RNAsubopt,RNA MoBOIP++)","$\Delta$MCC(RNAsubopt,Biokop)"] 1549 # "$\Delta$MCC(RNAsubopt,RNA MoBOIP++)","$\Delta$MCC(RNAsubopt,Biokop)"]
1549 # bplot = plt.boxplot(x, vert=False, patch_artist=True, notch=False, whis=[3,97]) 1550 # bplot = plt.boxplot(x, vert=False, patch_artist=True, notch=False, whis=[3,97])
1550 # for patch, color in zip(bplot['boxes'], colors): 1551 # for patch, color in zip(bplot['boxes'], colors):
......