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/dports/biology/jalview/jalview/test/jalview/datamodel/
H A DAlignedCodonIteratorTest.java69 assertEquals("P", codon.product); in testNext()
70 codon = codons.next(); in testNext()
73 codon = codons.next(); in testNext()
98 codon = codons.next(); in testNext_unmappedPeptide()
101 codon = codons.next(); in testNext_unmappedPeptide()
127 codon = codons.next(); in testNext_incompleteCodon()
152 codon = codons.next(); in testAnother()
155 codon = codons.next(); in testAnother()
158 codon = codons.next(); in testAnother()
182 codon = codons.next(); in testNext_withOffset()
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/codon/
H A DMG_REV.bf1 LoadFunctionLibrary("../codon.bf");
7 /** @module models.codon.MG_REV */
10 * @name models.codon.MG_REV.ModelDescription
16 codons = models.codon.MapCode(code);
101 * @name models.codon.MG_REV._DefineQ
157 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.alpha] = 1;
158 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.beta] = 0;
161 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.alpha] = 0;
162 … models.codon.MG_REV.set_branch_length.sub[models.codon.MG_REV.set_branch_length.beta] = 1;
221 …messages.log ("models.codon.MG_REV.set_branch_length: " + models.codon.MG_REV.set_branch_length.al…
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/dports/biology/py-biopython/biopython-1.79/Bio/Data/
H A DCodonTable.py246 c1, c2, c3 = codon
294 if {codon[0] for codon in codons}.issuperset(set(meanings))
299 if {codon[1] for codon in codons}.issuperset(set(meanings))
304 if {codon[2] for codon in codons}.issuperset(set(meanings))
312 if codon not in candidates and codon not in codons:
319 for codon in [
524 codon = codon.replace("T", "U")
533 if "T" in codon:
534 codon = codon.replace("T", "U")
541 if "T" in codon:
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_util.c385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA()
395 if (codon[0] & mapping[i]) { in s_CodonToAA()
431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local
443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation()
444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation()
445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation()
514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local
642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence()
790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence()
794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dblast_util.c385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA()
395 if (codon[0] & mapping[i]) { in s_CodonToAA()
431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local
443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation()
444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation()
445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation()
514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local
642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence()
790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence()
794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dblast_util.c385 if ((codon[0] | codon[1] | codon[2]) > 15) { in s_CodonToAA()
395 if (codon[0] & mapping[i]) { in s_CodonToAA()
431 Uint1 codon[CODON_LENGTH]; in BLAST_GetTranslation() local
443 codon[0] = nucl_seq[index]; in BLAST_GetTranslation()
444 codon[1] = nucl_seq[index+1]; in BLAST_GetTranslation()
445 codon[2] = nucl_seq[index+2]; in BLAST_GetTranslation()
514 int byte_value, codon=-1; in BLAST_TranslateCompressedSequence() local
642 codon = byte_value & 63; in BLAST_TranslateCompressedSequence()
790 codon = (byte_value & 63); in BLAST_TranslateCompressedSequence()
794 codon = (byte_value >> 2); in BLAST_TranslateCompressedSequence()
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/dports/biology/biolibc/biolibc-0.2.1/
H A Dorf.c57 long bl_next_start_codon(FILE *rna_stream, char codon[4]) in bl_next_start_codon()
66 codon[0] = codon[3] = '\0'; in bl_next_start_codon()
85 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_start_codon()
154 long bl_next_stop_codon(FILE *rna_stream, char codon[4]) in bl_next_stop_codon()
163 codon[0] = codon[3] = '\0'; in bl_next_stop_codon()
183 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_stop_codon()
196 codon[0] = ch1; codon[1] = ch2; codon[2] = ch3; in bl_next_stop_codon()
/dports/biology/wise/wise2.4.1/src/dynlibsrc/
H A Dcodon.dy113 codon c;
144 ct r codon table
164 ct r codon table
176 ct r codon table
189 ct r codon table
220 Tells you if this codon is a real codon
271 maps a 0-63 codon to a 0-123 codon. Suprisingly useful.
290 maps a 0-125 codon to a 0-63 codon.
294 c r codon 0-125
402 Reverses codon. Takes a forward codon number and
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H A Dcodon.pod102 returns amino acid for this codon number (NB codon numbers 0-125)
107 Argument c [READ ] codon number [codon]
120 Argument c [READ ] codon number [codon]
130 in this codon table
198 Tells you if this codon is a real codon
210 maps a 0-63 codon to a 0-123 codon. Suprisingly useful.
222 maps a 0-125 codon to a 0-63 codon.
228 Argument c [READ ] codon 0-125 [codon]
240 Argument c [READ ] codon number 0-124 [codon]
257 Argument c [READ ] codon number [codon]
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H A Dcodon.h16 typedef short int codon; typedef
127 aa Wise2_aminoacid_from_codon(CodonTable * ct,codon c);
143 int Wise2_aminoacid_no_from_codon(CodonTable * ct,codon c);
159 boolean Wise2_is_stop_codon(codon c,CodonTable * ct);
217 codon Wise2_codon_from_base4_codon(int c);
233 int Wise2_base4_codon_from_codon(codon c);
247 boolean Wise2_has_random_bases(codon c);
269 codon Wise2_permute_possible_random_bases(codon c,base one,base two,base three);
302 codon Wise2_reverse_codon(codon c);
319 base Wise2_base_from_codon(codon c,int pos);
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H A Dcodon.tex1 \section{codon} section in File Documentation
22 Tells you if this codon is a real codon
36 maps a 0-63 codon to a 0-123 codon. Suprisingly useful.
47 \item[c] [READ ] codon 0-125 [codon]
50 maps a 0-125 codon to a 0-63 codon.
64 \item[c] [READ ] codon number 0-124 [codon]
78 \item[c] [READ ] codon number [codon]
82 \item[returns] [UNKN ] codon number [codon]
315 \item[c] [READ ] codon number [codon]
318 returns amino acid for this codon number (NB codon numbers 0-125)
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H A Dcodon_api.h95 aa Wise2_aminoacid_from_codon( Wise2_CodonTable * ct,codon c);
109 boolean Wise2_is_stop_codon( codon c,Wise2_CodonTable * ct);
215 codon Wise2_codon_from_base4_codon( int c);
229 int Wise2_base4_codon_from_codon( codon c);
241 boolean Wise2_has_random_bases( codon c);
261 codon Wise2_permute_possible_random_bases( codon c,base one,base two,base three);
276 base Wise2_base_from_codon( codon c,int pos);
293 codon Wise2_codon_from_seq( char * seq);
H A Dcodon.c58 codon c; in read_CodonTable()
266 codon codon_from_base4_codon(int c) in codon_from_base4_codon()
324 boolean has_random_bases(codon c) in has_random_bases()
359 codon permute_possible_random_bases(codon c,base one,base two,base three) in permute_possible_random_bases()
430 codon reverse_codon(codon c) in reverse_codon()
501 codon codon_from_seq(char * seq) in codon_from_seq()
669 char codon[3]; in four_fold_sites_CodonTable() local
675 codon[0] = seq[0]; in four_fold_sites_CodonTable()
676 codon[1] = seq[1]; in four_fold_sites_CodonTable()
677 codon[2] = seq[2]; in four_fold_sites_CodonTable()
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/dports/biology/py-biopython/biopython-1.79/Bio/SeqUtils/
H A DCodonUsage.py115 for codon in codons:
116 total += self.codon_count[codon]
119 for codon in codons:
125 for codon_index, codon in enumerate(codons):
145 codon = dna_sequence[i : i + 3]
146 if codon in self.index:
148 if codon not in ["ATG", "TGG"]:
152 elif codon not in ["TGA", "TAA", "TAG"]:
173 codon = dna_sequence[i : i + 3]
174 if codon in self.codon_count:
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/dports/biology/wise/wise2.4.1/src/HMMer2/
H A Dtranslate.c51 int codon; /* index for codon */ in Translate() local
66 codon = 0; in Translate()
69 codon *= 4; in Translate()
72 case 'C': case 'c': codon += 1; break; in Translate()
73 case 'G': case 'g': codon += 2; break; in Translate()
74 case 'T': case 't': codon += 3; break; in Translate()
75 case 'U': case 'u': codon += 3; break; in Translate()
76 default: codon = 64; break; in Translate()
78 if (codon == 64) break; in Translate()
81 strcpy(aaptr, code[codon]); in Translate()
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/dports/biology/clustal-omega/clustal-omega-1.2.4/src/squid/
H A Dtranslate.c52 int codon; /* index for codon */ in Translate() local
67 codon = 0; in Translate()
70 codon *= 4; in Translate()
73 case 'C': case 'c': codon += 1; break; in Translate()
74 case 'G': case 'g': codon += 2; break; in Translate()
75 case 'T': case 't': codon += 3; break; in Translate()
76 case 'U': case 'u': codon += 3; break; in Translate()
77 default: codon = 64; break; in Translate()
79 if (codon == 64) break; in Translate()
82 strcpy(aaptr, code[codon]); in Translate()
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/
H A DtightString.c213 Codon codon; in readTightString() local
225 codon = tString->sequence[index]; in readTightString()
233 codon = tString->sequence[index]; in readTightString()
257 return (codon & 192) >> 6; in getNucleotide()
259 return (codon & 48) >> 4; in getNucleotide()
261 return (codon & 12) >> 2; in getNucleotide()
263 return (codon & 3); in getNucleotide()
293 Codon codon; in getNucleotideChar() local
301 return readNucleotide((codon & 48) >> 4); in getNucleotideChar()
305 return readNucleotide((codon & 3)); in getNucleotideChar()
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/dports/biology/velvet/velvet_1.2.10/src/
H A DtightString.c185 Codon codon; in readTightString() local
197 codon = tString->sequence[index]; in readTightString()
205 codon = tString->sequence[index]; in readTightString()
229 return (codon & 192) >> 6; in getNucleotide()
231 return (codon & 48) >> 4; in getNucleotide()
233 return (codon & 12) >> 2; in getNucleotide()
235 return (codon & 3); in getNucleotide()
265 Codon codon; in getNucleotideChar() local
273 return readNucleotide((codon & 48) >> 4); in getNucleotideChar()
275 return readNucleotide((codon & 12) >> 2); in getNucleotideChar()
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/
H A DtightString.c192 Codon codon; in readTightString() local
204 codon = tString->sequence[index]; in readTightString()
212 codon = tString->sequence[index]; in readTightString()
236 return (codon & 192) >> 6; in getNucleotide()
238 return (codon & 48) >> 4; in getNucleotide()
240 return (codon & 12) >> 2; in getNucleotide()
242 return (codon & 3); in getNucleotide()
272 Codon codon; in getNucleotideChar() local
280 return readNucleotide((codon & 48) >> 4); in getNucleotideChar()
282 return readNucleotide((codon & 12) >> 2); in getNucleotideChar()
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/dports/biology/py-hits/hits-0.1/hits/
H A Dgenetic_code.py7 def codon_sorting_key(codon): argument
8 return [nucleotide_to_index[b] for b in codon]
20 codon_to_index = {codon: i for i, codon in enumerate(all_codons)}
23 for codon in all_codons:
24 amino_acid = full_forward_table[codon]
26 full_back_table[amino_acid] = [codon]
28 full_back_table[amino_acid].append(codon)
34 for i, codon in enumerate(full_back_table[amino_acid]):
35 codon_to_amino_acid_and_index[codon] = (amino_acid, i)
99 for codon in anticodon_to_codons[anticodon]:
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/dports/biology/biolibc/biolibc-0.2.1/Man/
H A Dbl_next_start_codon.317 long bl_next_start_codon(FILE *rna_stream, char codon[4])
23 codon 4-character buffer to receive codon sequence
24 Set to "" if no codon found
36 codon). For example, givent the following input:
47 or EOF if no codon is found.
54 char codon[4];
58 printf("Start codon at %lu.n", pos);
59 if ( (pos = next_stop_codon(stdin, codon)) != EOF )
60 printf("Stop codon %s at %lu.n", codon, pos);
62 puts("No stop codon found.");
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H A Dbl_next_stop_codon.317 long bl_next_stop_codon(FILE *rna_stream, char codon[4])
23 codon 4-character buffer to receive codon sequence
24 Set to "" if no codon found
36 codon). For example, givent the following input:
47 or EOF if no codon is found.
54 char codon[4];
58 printf("Start codon at %lu.n", pos);
59 if ( (pos = next_stop_codon(stdin, codon)) != EOF )
60 printf("Stop codon %s at %lu.n", codon, pos);
62 puts("No stop codon found.");
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/
H A Dgenetic_code.bf107 lfunction genetic_code.partition_codon(codon) {
110 codon$16, (codon % 16) $4, codon % 4
141 for (codon = 0; codon < 64; codon += 1) {
142 if (genCode[codon] == stop_code) {
145 aa1 = genCode [codon];
172 * @returns returns ordered codon to amino acid map
191 * @returns whether or not the codon is a stop codon
193 lfunction genetic_code.IsStop(codon, code) {
276 for (codon = 0; codon < 64; codon += 1) {
279 if (genCode[codon] == stop_code) {
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dchips.c39 AjPCod codon; in main() local
57 codon = ajCodNewCodenum(0); in main()
68 ajCodSetTripletsS(codon,substr,&ccnt); in main()
71 ajCodCalcUsage(codon,ccnt); in main()
72 td = ajCodCalcNc(codon); in main()
76 ajCodClearData(codon); in main()
82 ajCodCalcUsage(codon,ccnt); in main()
83 td = ajCodCalcNc(codon); in main()
91 ajCodDel(&codon); in main()
H A Dcusp.c39 AjPCod codon; in main() local
53 codon = ajCodNewCodenum(0); in main()
54 ajCodSetNameS(codon, ajFileGetPrintnameS(outf)); in main()
61 ajCodSetTripletsS(codon,substr,&ccnt); in main()
64 ajCodCalcUsage(codon,ccnt); in main()
66 ajCodSetDescC(codon, "CUSP codon usage file"); in main()
67 ajCodWrite(codon, outf); in main()
71 ajCodDel(&codon); in main()

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