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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/
H A Dgenetic_code.bf6 /** @module genetic_code */
10 genetic_code.nucleotides = "ACGT";
16 genetic_code.stop_code = 10;
28 genetic_code.singleAALetterToFullName = {
56 * genetic_code.DefineCodonToAAGivenCode
75 function genetic_code.CountSense(code) {
164 return {^"terms.genetic_code.synonymous" : SS, ^"terms.genetic_code.nonsynonymous" : NS};
169 * genetic_code.DefineCodonToAAMapping
187 * genetic_code.IsStop
188 * @name genetic_code.IsStop
[all …]
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/sequence/
H A D_rna.py216 def translate(self, genetic_code=1, *args, **kwargs): argument
281 if not isinstance(genetic_code, skbio.GeneticCode):
282 genetic_code = skbio.GeneticCode.from_ncbi(genetic_code)
283 return genetic_code.translate(self, *args, **kwargs)
286 def translate_six_frames(self, genetic_code=1, *args, **kwargs): argument
412 if not isinstance(genetic_code, skbio.GeneticCode):
413 genetic_code = skbio.GeneticCode.from_ncbi(genetic_code)
414 return genetic_code.translate_six_frames(self, *args, **kwargs)
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/
H A DNuc_translator.pm131 my ($genetic_code) = @_;
133 &use_specified_genetic_code($genetic_code);
595 foreach my $genetic_code (sort keys %expected_translation_tables) {
596 my $expected_translation = $expected_translation_tables{$genetic_code};
603 print "$genetic_code\tOK\n";
606 print "\n$genetic_code\tERROR:\n"
622 my $genetic_code = $ARGV[0];
624 if ($genetic_code eq "TEST") {
628 if ($genetic_code) {
629 print "\nTranslation table for $genetic_code:\n\n";
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dorf.cpp124 int genetic_code, in FindForwardOrfs() argument
133 objects::CGen_code_table::GetTransTable(genetic_code); in FindForwardOrfs()
229 int genetic_code, in s_FindOrfs() argument
303 objects::CGen_code_table::GetTransTable(genetic_code); in GetStartCodons()
339 int genetic_code, in FindOrfs() argument
345 genetic_code, allowable_starts, longest_orfs, max_seq_gap); in FindOrfs()
354 int genetic_code, in FindOrfs() argument
360 genetic_code, allowable_starts, longest_orfs, max_seq_gap); in FindOrfs()
369 int genetic_code, in FindOrfs() argument
390 int genetic_code, in FindStrongKozakUOrfs() argument
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dorf.hpp79 int genetic_code = 1,
87 int genetic_code = 1,
95 int genetic_code = 1,
102 static vector<string> GetStartCodons(int genetic_code, bool include_atg, bool include_alt);
114 int genetic_code = 1,
139 MakeCDSAnnot(const TLocVec& orfs, int genetic_code = 1,
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/
H A Dcodon.bf1 LoadFunctionLibrary ("../tasks/genetic_code.bf");
8 * @param {String} genetic_code
11 function models.codon.MapCode (genetic_code) {
13 …turn {terms.sense_codons : utility.UniqueValues (genetic_code.ComputeCodonCodeToStringMap (genetic…
14 …terms.stop_codons : utility.UniqueValues (genetic_code.ComputeCodonCodeToStringMapStop (genetic_c…
15 terms.translation_table : genetic_code.DefineCodonToAAGivenCode (genetic_code) };
151 …* @param {String} type - terms.genetic_code.synonymous or terms.genetic_code.nonsynonymous or call…
167 if (type == utility.getGlobalValue("terms.genetic_code.synonymous")) {
170 if (type == utility.getGlobalValue("terms.genetic_code.non_synonymous")) {
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/SelectionAnalyses/modules/
H A Dselection_lib.ibf10 * @param {AssociativeList} genetic_code
34 …on.substitution_mapper (matrix, tree, ambig_lookup, pairwise_counts, code_to_codon, genetic_code) {
39 aa_mapping = genetic_code.DefineCodonToAAMapping (genetic_code);
40 integer_mapping = genetic_code.DefineIntegerToAAMapping (genetic_code, TRUE);
82 …ub_count")]) [s] = (pairwise_counts[utility.getGlobalValue("terms.genetic_code.OPS")])[parent_…
83 …us_sub_count")]) [s] = (pairwise_counts[utility.getGlobalValue("terms.genetic_code.OPN")])[parent_…
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/
H A DTransDecoder.Predict31 my $genetic_code = "Universal";
182 'G=s' => \$genetic_code,
214 if ($genetic_code) {
215 $genetic_code = " --genetic_code $genetic_code";
361 …gff3_file_to_proteins.pl --gff3 $gff3_file --fasta $transcripts_file $genetic_code > $best_pep_fil…
367 …roteins.pl --gff3 $gff3_file --fasta $transcripts_file --seqType CDS $genetic_code > $best_cds_fil…
H A DTransDecoder.LongOrfs32 my $genetic_code='universal';
97 'G=s' => \$genetic_code,
127 if ($genetic_code ne 'universal') {
128 &Nuc_translator::use_specified_genetic_code($genetic_code);
349 …my $pep_header = ">$model_id type:$prot_type len:$length gc:$genetic_code $acc:$start-$stop($orien…
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/
H A Dgff3_file_to_proteins.pl50 my $genetic_code = '';
55 'genetic_code=s' => \$genetic_code,
66 if ($genetic_code) {
67 &Nuc_translator::use_specified_genetic_code($genetic_code);
/dports/biology/seaview/seaview/csrc/
H A Dmisc_acnuc.c81 struct genetic_code_libel genetic_code[TOTCODES] = variable
471 return genetic_code[code].libel ; in get_code_descr()
484 return genetic_code[code].target ; in get_code_target()
526 pdata = &genetic_code[code]; /* ici ecriture plus compacte mal compilee sur PC*/ in codaa()
533 return genetic_code[gc].ncbi_gc; in get_ncbi_gc_number()
542 if(genetic_code[num].ncbi_gc == ncbi_gc) return num; in get_acnuc_gc_number()
684 pdata = &genetic_code[gc]; in init_codon_to_aa()
701 pdata = &genetic_code[gc]; in stop_codon_to_aa()
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/
H A DchooseGeneticCode.def131 genetic_code.stop_code = 10;
589 if (code[_ci] == genetic_code.stop_code) {
637 return code[codon] == ^ "genetic_code.stop_code";
677 if (genCode[_idx] != ^ "genetic_code.stop_code") {
690 if (genCode[_idx] == ^ "genetic_code.stop_code") {
699 lfunction genetic_code.partition_codon(codon) {
707 lfunction genetic_code.assemble_codon(positions) {
713 lfunction genetic_code.ComputeBranchLengthStencils(genCode) {
729 stop_code = ^ "genetic_code.stop_code";
762 lfunction genetic_code.DefineCodonToAAMapping (code) {
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/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/
H A Dalignment.cpp67 genetic_code = NULL; in Alignment()
517 ASSERT(genetic_code); in isStopCodon()
523 ASSERT(genetic_code); in getNumNonstopCodons()
2787 genetic_code = aln->genetic_code; in extractSubAlignment()
2840 genetic_code = aln->genetic_code; in extractPatterns()
2880 genetic_code = aln->genetic_code; in extractPatternFreqs()
2922 genetic_code = aln->genetic_code; in extractSites()
3268 genetic_code = aln->genetic_code; in createBootstrapAlignment()
3533 genetic_code = aln.genetic_code; in buildFromPatternFreq()
3576 genetic_code = aln->genetic_code; in createGapMaskedAlignment()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_aux.cpp109 ddc.Log("genetic_code", m_Ptr->genetic_code); in DebugDump()
588 FindGeneticCode(int genetic_code) in FindGeneticCode() argument
631 if ( !genetic_code ) { in CAutomaticGenCodeSingleton()
632 genetic_code = BLAST_GENETIC_CODE; in CAutomaticGenCodeSingleton()
639 if (GenCodeSingletonFind(genetic_code) == NULL) { in CAutomaticGenCodeSingleton()
640 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in CAutomaticGenCodeSingleton()
641 GenCodeSingletonAdd(genetic_code, gc.get()); in CAutomaticGenCodeSingleton()
653 void CAutomaticGenCodeSingleton::AddGeneticCode(int genetic_code) in AddGeneticCode() argument
656 if (GenCodeSingletonFind(genetic_code) == NULL) { in AddGeneticCode()
657 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in AddGeneticCode()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_aux.cpp109 ddc.Log("genetic_code", m_Ptr->genetic_code); in DebugDump()
588 FindGeneticCode(int genetic_code) in FindGeneticCode() argument
631 if ( !genetic_code ) { in CAutomaticGenCodeSingleton()
632 genetic_code = BLAST_GENETIC_CODE; in CAutomaticGenCodeSingleton()
639 if (GenCodeSingletonFind(genetic_code) == NULL) { in CAutomaticGenCodeSingleton()
640 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in CAutomaticGenCodeSingleton()
641 GenCodeSingletonAdd(genetic_code, gc.get()); in CAutomaticGenCodeSingleton()
653 void CAutomaticGenCodeSingleton::AddGeneticCode(int genetic_code) in AddGeneticCode() argument
656 if (GenCodeSingletonFind(genetic_code) == NULL) { in AddGeneticCode()
657 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in AddGeneticCode()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_options_api.c89 BLAST_GeneticCodeFind(db_options->genetic_code, &gc); in SBlastOptionsNew()
90 GenCodeSingletonAdd(db_options->genetic_code, gc); in SBlastOptionsNew()
324 options->db_options->genetic_code = gc; in SBlastOptionsSetDbGeneticCode()
329 BLAST_GeneticCodeFind(options->db_options->genetic_code, &gcode); in SBlastOptionsSetDbGeneticCode()
330 GenCodeSingletonAdd(options->db_options->genetic_code, gcode); in SBlastOptionsSetDbGeneticCode()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_util.h180 const Uint1* genetic_code);
290 Int4 nucl_length, const Uint1* genetic_code,
309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_util.h180 const Uint1* genetic_code);
290 Int4 nucl_length, const Uint1* genetic_code,
309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
H A Dblast_util.c429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument
446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation()
1004 if (genetic_code == NULL) in s_BlastGetTranslationTable()
1029 genetic_code[codon]; in s_BlastGetTranslationTable()
1036 genetic_code[codon]; in s_BlastGetTranslationTable()
1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument
1070 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations()
1071 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations()
1093 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations()
1140 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_util.h180 const Uint1* genetic_code);
290 Int4 nucl_length, const Uint1* genetic_code,
309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
/dports/biology/p5-Bio-DB-NCBIHelper/Bio-DB-NCBIHelper-1.7.7/bin/
H A Dbp_query_entrez_taxa54 print " genetic_code ", $node->genetic_code, "\n";
70 print " genetic_code ", $node->genetic_code, "\n";
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_util.c429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument
446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation()
1004 if (genetic_code == NULL) in s_BlastGetTranslationTable()
1029 genetic_code[codon]; in s_BlastGetTranslationTable()
1036 genetic_code[codon]; in s_BlastGetTranslationTable()
1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument
1072 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations()
1073 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations()
1095 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations()
1142 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_util.c429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument
446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation()
1004 if (genetic_code == NULL) in s_BlastGetTranslationTable()
1029 genetic_code[codon]; in s_BlastGetTranslationTable()
1036 genetic_code[codon]; in s_BlastGetTranslationTable()
1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument
1070 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations()
1071 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations()
1093 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations()
1140 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument
[all …]
/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/
H A Dmodels-codon.bf6 genetic_code = {
10 mapped_code = models.codon.MapCode (genetic_code);
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsuggest.c225 static Char *genetic_code = NULL; variable
445 if (genetic_code == NULL) { in get_frames()
446 genetic_code = suggestRec.geneticCode; in get_frames()
462 frame[i][j] = genetic_code[val] ; in get_frames()
515 genetic_code = NULL; in ClearBatchSuggestFrames()
1071 if ( ! genetic_code){ in APT_suggest()
1075 if ( ! * genetic_code){ in APT_suggest()
1136 fix_single_unassigned(dna_seq, rev_seq, p_seq, genetic_code); in APT_suggest()
1139 fix_overlaps_by_splice_sites(dna_seq, rev_seq, p_seq, genetic_code); in APT_suggest()
1422 genetic_code = geneticCode; in Suggest_Intervals()
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