/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/ |
H A D | PrimarySeqI.pm | 583 $complete_codons, $throw, $codonTable, $orf, $start_codon, $offset); 588 $complete_codons, $throw,$codonTable, $orf, $start_codon, $offset) = 629 if ($start_codon) { 630 $self->throw("Invalid start codon: $start_codon.") if 631 ( $start_codon !~ /^[A-Z]{3}$/i ); 646 …my ($orf_region) = $self->_find_orfs_nucleotide( $seq, $codonTable, $start_codon, $orf eq 'longest… 896 my ( $self, $sequence, $codon_table, $start_codon, $first_only ) = @_; 898 $start_codon = uc $start_codon if $start_codon; 900 my $is_start = $start_codon 901 ? sub { shift eq $start_codon }
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gtfwriter_test_cases/ |
H A D | rw-836-3.entry.gtf | 7 AP000423.1 DDBJ start_codon 1442 1444 . - 0 gene_id "psbA"; transcript_id "unassigned_transcript_2"… 21 AP000423.1 DDBJ start_codon 6186 6188 . - 0 gene_id "rps16"; transcript_id "unassigned_transcript_5… 28 AP000423.1 DDBJ start_codon 7017 7019 . + 0 gene_id "psbK"; transcript_id "unassigned_transcript_7"… 32 AP000423.1 DDBJ start_codon 7583 7585 . + 0 gene_id "psbI"; transcript_id "unassigned_transcript_8"… 52 AP000423.1 DDBJ start_codon 12796 12798 . - 0 gene_id "atpF"; transcript_id "unassigned_transcript_… 60 AP000423.1 DDBJ start_codon 14768 14770 . - 0 gene_id "atpI"; transcript_id "unassigned_transcript_… 84 AP000423.1 DDBJ start_codon 28089 28091 . + 0 gene_id "ycf6"; transcript_id "unassigned_transcript_… 115 AP000423.1 DDBJ start_codon 35751 35753 . + 0 gene_id "ycf9"; transcript_id "unassigned_transcript_… 138 AP000423.1 DDBJ start_codon 43749 43751 . - 0 gene_id "ycf3"; transcript_id "unassigned_transcript_… 200 AP000423.1 DDBJ start_codon 59772 59774 . + 0 gene_id "ycf4"; transcript_id "unassigned_transcript_… [all …]
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H A D | rw-836-1.entry.gtf | 5 NC_016163.1 RefSeq start_codon 262300 262302 . + 0 gene_id "phiR1-37_gp367"; transcript_id "unassig… 9 NC_016163.1 RefSeq start_codon 103 105 . + 0 gene_id "phiR1-37_gp001"; transcript_id "unassigned_tr… 13 NC_016163.1 RefSeq start_codon 326 328 . + 0 gene_id "phiR1-37_gp002"; transcript_id "unassigned_tr… 17 NC_016163.1 RefSeq start_codon 564 566 . + 0 gene_id "phiR1-37_gp003"; transcript_id "unassigned_tr… 21 NC_016163.1 RefSeq start_codon 784 786 . + 0 gene_id "phiR1-37_gp004"; transcript_id "unassigned_tr… 25 NC_016163.1 RefSeq start_codon 999 1001 . + 0 gene_id "phiR1-37_gp005"; transcript_id "unassigned_t… 29 NC_016163.1 RefSeq start_codon 1181 1183 . + 0 gene_id "phiR1-37_gp006"; transcript_id "unassigned_… 33 NC_016163.1 RefSeq start_codon 1531 1533 . + 0 gene_id "phiR1-37_gp007"; transcript_id "unassigned_… 37 NC_016163.1 RefSeq start_codon 1736 1738 . + 0 gene_id "phiR1-37_gp008"; transcript_id "unassigned_… 41 NC_016163.1 RefSeq start_codon 1918 1920 . + 0 gene_id "phiR1-37_gp009"; transcript_id "unassigned_… [all …]
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H A D | rw-836-2.entry.gtf | 130 AJ507799.2 EMBL start_codon 40267 40269 . - 0 gene_id "unassigned_gene_2"; transcript_id "unassigne… 214 AJ507799.2 EMBL start_codon 68830 68832 . + 0 gene_id "BMRF2"; transcript_id "unassigned_transcript… 229 AJ507799.2 EMBL start_codon 71998 72000 . - 0 gene_id "BSLF2"; transcript_id "unassigned_transcript… 267 AJ507799.2 EMBL start_codon 77723 77725 . - 0 gene_id "BLLF2"; transcript_id "unassigned_transcript… 431 AJ507799.2 EMBL start_codon 118776 118778 . - 0 gene_id "BDLF3"; transcript_id "unassigned_transcri… 436 AJ507799.2 EMBL start_codon 120099 120101 . - 0 gene_id "BDLF2"; transcript_id "unassigned_transcri… 480 AJ507799.2 EMBL start_codon 135625 135627 . - 0 gene_id "BVLF1"; transcript_id "unassigned_transcri… 515 AJ507799.2 EMBL start_codon 150323 150325 . + 0 gene_id "RPMS1"; transcript_id "unassigned_transcri… 522 AJ507799.2 EMBL start_codon 143342 143344 . - 0 gene_id "LF3"; transcript_id "unassigned_transcript… 534 AJ507799.2 EMBL start_codon 152639 152641 . - 0 gene_id "BILF1"; transcript_id "unassigned_transcri… [all …]
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H A D | rw-484.entry.gtf | 6 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001346715.1"; db_x… 10 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001346717.1"; db_x… 14 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001346713.1"; db_x… 18 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001099401.1"; db_x… 22 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_003919.2"; db_xref… 26 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001099400.1"; db_x… 30 NG_011340.1 RefSeq start_codon 4772 4774 . - 0 gene_id "SGCE"; transcript_id "NM_001301139.1"; db_x… 37 NG_011340.1 RefSeq start_codon 5263 5265 . + 0 gene_id "PEG10"; transcript_id "NM_001172438.2"; db_… 43 NG_011340.1 RefSeq start_codon 12233 12235 . + 0 gene_id "PEG10"; transcript_id "NM_001040152.1"; d… 50 NG_011340.1 RefSeq start_codon 12233 12235 . + 0 gene_id "PEG10"; transcript_id "NM_015068.3"; db_x…
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/dports/biology/p5-Bio-GFF3/Bio-GFF3-2.0/t/data/ |
H A D | au9_scaffold_subset.gff3 | 5 Group1.36 AU9 start_codon 177110 177112 . + 0 Parent=au9.g1002.t1 26 Group1.36 AU9 start_codon 166797 166799 . - 0 Parent=au9.g999.t1 35 Group1.36 AU9 start_codon 110078 110080 . + 0 Parent=au9.g989.t2 51 Group1.36 AU9 start_codon 110055 110057 . + 0 Parent=au9.g989.t1 135 Group1.36 AU9 start_codon 59976 59978 . - 0 Parent=au9.g986.t1 157 Group1.36 AU9 start_codon 36769 36771 . - 0 Parent=au9.g985.t1 178 Group1.36 AU9 start_codon 78956 78958 . - 0 Parent=au9.g987.t1 280 Group1.36 AU9 start_codon 1859 1861 . + 0 Parent=au9.g984.t1 302 Group1.36 AU9 start_codon 2079 2081 . + 0 Parent=au9.g984.t2 324 Group1.36 AU9 start_codon 7973 7975 . + 0 Parent=au9.g984.t4 [all …]
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H A D | Saccharomyces_cerevisiae_EF3_e64.gff3 | 5 XIII protein_coding start_codon 230811 230813 . - 0 ID=start_codon:YML021C:1;Parent=YML021C
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/import/unit_test/data/input/ |
H A D | test-classified-exons.gtf | 11 140 Twinscan start_codon 71805 71806 . - 0 gene_id "140.000"; transcript_id "140.000.1"; 12 140 Twinscan start_codon 73222 73222 . - 2 gene_id "140.000"; transcript_id "140.000.1";
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H A D | rw-100.gtf | 8 Contig602 AUGUSTUS start_codon 682 684 . - 0 transcript_id "g15.t1"; gene_id "g15"; 11 Contig602 AUGUSTUS start_codon 1399 1401 . + 0 transcript_id "g16.t1"; gene_id "g16";
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H A D | uud-3s.gtf | 4 8 protein_coding start_codon 28905 28907 . + 0 gene_id "ENSG00000253896"; transcript_id "ENST000005… 9 8 protein_coding start_codon 28905 28907 . + 0 gene_id "ENSG00000253896"; transcript_id "ENST000005…
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H A D | test-only-cds.gtf | 4 381 Twinscan start_codon 380 382 . + 0 gene_id "001"; transcript_id "001.1";
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H A D | test-unclassified-exons.gtf | 9 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
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H A D | exon-cds.gtf | 11 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
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H A D | rw-451.gtf | 2 chr1 FINAL_GENE_SET start_codon 11499 11501 . - 0 gene_id "CNAG_00001"; locus_tag "XNAG_00001"; tr…
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/example/ |
H A D | dmel.gtf | 3 2L dm3_flyBaseGene start_codon 8386247 8386249 0.000000 + . gene_id "CG13384-RD"; transcript_id "CG… 14 2L dm3_flyBaseGene start_codon 8384860 8384862 0.000000 + . gene_id "CG13384-RC"; transcript_id "CG… 28 2L dm3_flyBaseGene start_codon 8386247 8386249 0.000000 + . gene_id "CG13384-RE"; transcript_id "CG… 41 2L dm3_flyBaseGene start_codon 8386247 8386249 0.000000 + . gene_id "CG13384-RG"; transcript_id "CG… 54 2L dm3_flyBaseGene start_codon 8386247 8386249 0.000000 + . gene_id "CG13384-RF"; transcript_id "CG… 1002 2L dm3_flyBaseGene start_codon 7680 7682 0.000000 + . gene_id "CG11023-RA"; transcript_id "CG11023-… 1099 2L dm3_flyBaseGene start_codon 15646 15648 0.000000 - . gene_id "CG2671-RD"; transcript_id "CG2671-… 1100 2L dm3_flyBaseGene start_codon 15646 15648 0.000000 - . gene_id "CG2671-RE"; transcript_id "CG2671-… 1101 2L dm3_flyBaseGene start_codon 15646 15648 0.000000 - . gene_id "CG2671-RF"; transcript_id "CG2671-… 1106 2L dm3_flyBaseGene start_codon 17134 17136 0.000000 - . gene_id "CG2671-RA"; transcript_id "CG2671-… [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases_genbank/ |
H A D | rw-451_LSVZ_Augustus.gff3 | 5 scaffold12159 AUGUSTUS start_codon 980 982 . - 0 Parent=scaffold12159.g1.t1;product=dtw domain-cont… 10 scaffold12159 AUGUSTUS start_codon 3820 3822 . + 0 Parent=scaffold12159.g2.t1;product=dtw domain-co… 13 scaffold12160 AUGUSTUS start_codon 646 648 . + 0 Parent=scaffold12160.g1.t1;product=pyruvate dehydr…
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/dports/biology/py-crossmap/CrossMap-0.5.4/test/ |
H A D | test08_hg19.gtf | 45 chr1 hg19_refGene start_codon 204913444 204913446 0.000000 + . gene_id "NM_015090"; transcript_id "… 100 chr1 hg19_refGene start_codon 173446537 173446539 0.000000 + . gene_id "NM_004905"; transcript_id "… 152 chr2 hg19_refGene start_codon 192141622 192141624 0.000000 + . gene_id "NM_012223"; transcript_id "… 180 chr2 hg19_refGene start_codon 230924066 230924068 0.000000 - . gene_id "NM_152527"; transcript_id "… 256 chr4 hg19_refGene start_codon 76928600 76928602 0.000000 - . gene_id "NM_002416"; transcript_id "NM… 352 chr6 hg19_refGene start_codon 74161902 74161904 0.000000 - . gene_id "NM_138441"; transcript_id "NM… 436 chr8 hg19_refGene start_codon 33370129 33370131 0.000000 - . gene_id "NM_025115"; transcript_id "NM… 446 chr9 hg19_refGene start_codon 178967 178969 0.000000 - . gene_id "NM_018491"; transcript_id "NM_018… 469 chr9 hg19_refGene start_codon 35689812 35689814 0.000000 - . gene_id "NM_213674"; transcript_id "NM… 513 chrX hg19_refGene start_codon 7811245 7811247 0.000000 + . gene_id "NM_013452"; transcript_id "NM_0… [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gtfreader_test_cases/ |
H A D | rw-100.gtf | 8 Contig602 AUGUSTUS start_codon 682 684 . - 0 transcript_id "g15.t1"; gene_id "g15"; 11 Contig602 AUGUSTUS start_codon 1399 1401 . + 0 transcript_id "g16.t1"; gene_id "g16";
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H A D | exon-cds.gtf | 11 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
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/dports/biology/py-gffutils/gffutils-0.10.1/gffutils/test/data/ |
H A D | FBgn0031208.gtf | 27 chr2L protein_coding start_codon 7680 7682 . + 0 gene_id "FBgn0031208"; transcript_id "FBtr0300689"; 28 chr2L protein_coding start_codon 7680 7682 . + 0 gene_id "FBgn0031208"; transcript_id "FBtr0300690"; 107 chr2L FAKE start_codon 10000 11002 . - . gene_id "Fk_gene_1"; transcript_id "transcript_Fk_gene_1";
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/PWM/__deprecated/ |
H A D | build_atgPWM.pl | 90 my $start_codon = substr($transcript_seq, $start_coord - 1, 3); 91 if ($start_codon ne "ATG") { next; }
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/PWM/ |
H A D | build_atgPWM_+-.pl | 99 my $start_codon = substr($transcript_seq, $start_coord - 1, 3); 100 if ($start_codon ne "ATG") { next; }
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/dports/biology/bedtools/bedtools2-2.30.0/test/map/ |
H A D | test.gff | 1 chr1 hg19_ccdsGene start_codon 1 9 0.000000 + . gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/manual/source/Tutorial/DataStructures/Store/ |
H A D | assignment_annotations.gtf | 9 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/genome_annotations/ |
H A D | assignment_annotations.gtf | 9 381 Twinscan start_codon 380 382 . + 0 gene_id "381.000"; transcript_id "381.000.1";
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