Toggle navigation
Toggle navigation
This project
Loading...
Sign in
Louis BECQUEY
/
biorseo
Go to a project
Toggle navigation
Toggle navigation pinning
Projects
Groups
Snippets
Help
Project
Activity
Repository
Pipelines
Graphs
Issues
0
Merge Requests
0
Network
Create a new issue
Builds
Commits
Authored by
Louis BECQUEY
2019-06-17 10:43:47 +0200
Browse Files
Options
Browse Files
Download
Email Patches
Plain Diff
Commit
91a8d2f84cbc52909b628e6bad9653964a49917a
91a8d2f8
1 parent
a86eaa30
random small fixes
Show whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
1 additions
and
106 deletions
data/sec_structs/applications.dbn
data/sec_structs/verified_tRNAs.dbn
doc/fig/pseudobase.jpg
test_on_RNAstrand.py
data/sec_structs/applications.dbn
View file @
91a8d2f
data/sec_structs/verified_tRNAs.dbn
deleted
100644 → 0
View file @
a86eaa3
>>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_TRNA-NEOMYCIN_COMPLEX_'_(PDB_00095)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGACUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
(((((((..((((........))))(((((........)))))....(((((.......))))))))))))....
>>__'YEAST_INITIATOR_TRNA_'_(PDB_00229)
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA
(((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))))....
>>__'THE_CRYSTAL_STRUCTURE_OF_PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_COGNATE_TRNAPHE_'_(PDB_00362)
GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA-GLN_MUTANT_AND_AN_ACTIVE-SITE_INHIBITOR_'_(PDB_00373)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))..(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA_MUTANT_AND_AN_ACTIVE_SITE_INHIBITOR_'_(PDB_00374)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))...(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))...(((((.......))))))))))).....
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00402)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'STRUCTURAL_BASIS_OF_ANTICODON_LOOP_RECOGNITION_BY_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00425)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
>>__'STRUCTURAL_BASIS_FOR_TRANSFER_RNA_AMINOACEYLATION_BY_ESCHERICHIA_COLI_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00426)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........))).(((((((...))))))).....(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEAL_TYROSYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA(TYR)_AND_L-TYROSINE_'_(PDB_00474)
CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA
(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMINE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00620)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMATE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00621)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_THE_TRNA_DOMAIN_OF_TRANSFER-MESSENGER_RNA_IN_COMPLEX_WITH_SMPB_'_(PDB_00637)
GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGCUCGACGGGGACUUCGGUCCUCGGA
......((((((((....))))))))..(((((.......)))))...((((((((....)))))))).
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235N_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00669)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235G_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00670)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))(((((((.....)))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_I129T_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00671)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((.......))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA_AND_AN_AMINO_ACID_ANALOG_'_(PDB_00672)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00673)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00674)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'CRYSTAL_STRUCTURE_OF_CYSTEINYL-TRNA_SYNTHETASE_BINARY_COMPLEX_WITH_TRNACYS_'_(PDB_00742)
GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA
(((((((..(((.........))).((((((.....))))))....(((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_TRNA_NUCLEOTIDYLTRANSFERASE_COMPLEXED_WITH_A_PRIMER_TRNA_AND_AN_INCOMING_ATP_ANALOG_'_(PDB_00767)
GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCGGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACCAA
(((((((.(((.........))).)))))))(((((((.(((.........))).))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_TO_GLUTAMINE_AND_2\'DEOXY_A76_GLUTAMINE_TRNA_'_(PDB_00901)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'IF2,_IF1,_AND_TRNA_FITTED_TO_CRYO-EM_DATA_OF_E._COLI_70S_INITIATION_COMPLEX_'_(PDB_00903)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_00926)
GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCA
((.((((..(((((.....)))))...((((.....)))).......(((((.......))))))))).)).
>>__'CRYSTAL_STRUCTURE_OF_STAPHYLOCOCCUS_AUREUS_TRNA_ADENOSINE_DEAMINASE,_TADA,_IN_COMPLEX_WITH_RNA_'_(PDB_00943)
UUGACUACGGAUCAAUUGACUACGGAUCAAGACUACGGUUUGACUACGGAUCAA
(((((.....)))))(((((.....))))).........(((((.....)))))
>>__'COCRYSTAL_STRUCTURE_OF_AN_RNA_SULFURATION_ENZYME_MNMA_AND_TRNA-GLU_IN_THE_PRE-REACTION_STATE_'_(PDB_00999)
GUCCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG
..((.....(((((.......)))))(((((((.....)))))))....((((.......))))...)).
>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_01002)
GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCACCA
(((((((....(((.....)))...((((((.....)))))).....(((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_AND_O-PHOSPHOSERINE_'_(PDB_01009)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
((((((([[(((]].......)))..((((.......))))......(((((.......))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_'_(PDB_01010)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
..((((([[(((]].......)))..(((((.....)))))......(((((.......))))))))))..
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAOPAL_AND_O-PHOSPHOSERINE_("OPAL_COMPLEX")_'_(PDB_01011)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUUCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAAMBER_AND_O-PHOSPHOSERINE_("AMBER_COMPLEX")_'_(PDB_01012)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUCUAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_RNASE_Z/TRNA(THR)_COMPLEX_'_(PDB_01053)
GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU
(((((((..((((........))))...(((((.......)))))))))))).
>>__'PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_TRNA_AND_A_PHENYLALANYL-ADENYLATE_ANALOG_'_(PDB_01134)
GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
(((((((....((........))...((((((.....)))))).....((((.........)))))))))))....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE_'_(PDB_01258)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE_'_(PDB_01259)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
doc/fig/pseudobase.jpg
View file @
91a8d2f
102 KB
|
W:
|
H:
131 KB
|
W:
|
H:
2-up
Swipe
Onion skin
test_on_RNAstrand.py
View file @
91a8d2f
...
...
@@ -312,7 +312,7 @@ def launch_BayesPairing(module_type, seq_, header_, basename):
rna
.
close
()
def
launch_RNAMoIP_worker
(
x
):
RNAMoIP
=
"../RNAMoIP
/RNAMoIP.py"
RNAMoIP
=
biorseoDir
+
"/../RNAMoIP/Src
/RNAMoIP.py"
logfile
=
open
(
"log_of_the_run.sh"
,
'a'
)
logfile
.
write
(
" "
.
join
([
"gurobi.sh"
,
RNAMoIP
,
"-s"
,
'"'
+
x
[
1
]
+
'"'
,
"-ss"
,
'"'
+
x
[
0
]
.
strip
()
+
'"'
,
"-d"
,
descfolder
]))
logfile
.
write
(
"
\n
"
)
...
...
Please
register
or
login
to post a comment