C-RCPred: Constrained RNA Complex Prediction
C-RCPred is an open-source bioinformatics program for the prediction of RNA complexes.
The multi-objective algorithm is implemented in C++ and runs on UNIX-like operating systems.
Besides this stand-alone version, a web server is freely available on the EvryRNA platform.
If all the dependencies are already installed on your system, using the
make command within the C-RCPred directory is sufficient to build the executable file.
Alternatively, C-RCPred can easily be installed by using Docker as follows:
git clone https://forge.ibisc.univ-evry.fr/EvryRNA/C-RCPred.git cd C-RCPred docker build -t c-rcpred ./
docker build command has been tested for Docker version 20.10.7.
The installation of C-RCPred depends on two bioinformatics libraries:
Two sets of files are provided to test C-RCPred. Each set contains 4 input files (.fasta, .txt30, .txt90, and .txt).
Thus, an example of command is:
./C-RCPred -f test/NDB_00016.fasta \ -s test/NDB_00016_str.txt30 \ -i test/NDB_00016_inter.txt90 \ -p test/NDB_00016_probing.txt \ -l 20 -u 80 -t 100 -e 1 \ -g NDB_00016_graph.txt \ -q NDB_00016_cliques.txt -m 20
This command will output predicted secondary structures, represented with the dot-bracket notation.
Other results will be written in the NDB_00016_graph.txt and NDB_00016_cliques.txt files (see options below).
A similar test can be performed with the files provided for PDB_00805.
The following list of options can be accessed by running
-f Input fasta file -s Input secondary structure files, -i Input interaction secondary structure files, -c Constraint files where constraints are in the same order than the secondary structure and interaction files -p Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed) -o Format of output "d" (dot-parenthesis, default), "j" (JSON) or "b" (base pair list format) -e Energy model (0: No energy model; use energies computed by upstream tools, 1: ViennaRNA package model; default, 2: NUPACK model) -t Threshold for compatibility RNA (0->100, default 100) -l Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account) -u Upper probing threshold (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account) -g Output graph file -k Output cliques predicted -q Output cliques predicted without duplicates -m Maximum number of structures to output
Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA. NUPACK: Analysis and design of nucleic acid systems Journal of Computational Chemistry, 2011, doi:10.1002/jcc.21596 ↩