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Searched refs:exon1 (Results 1 – 25 of 34) sorted by relevance

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/dports/biology/bbmap/bbmap/current/dna/
H A DExon.java56 public static Exon merge(Exon exon1, Exon exon2){ in merge() argument
57 assert(canMerge(exon1, exon2)); in merge()
58 …return new Exon(min(exon1.a, exon2.a), max(exon1.b, exon2.b), exon1.chromosome, exon1.strand, exon… in merge()
61 public static boolean canMerge(Exon exon1, Exon exon2){ in canMerge() argument
62 if(exon1.chromosome!=exon2.chromosome){return false;} in canMerge()
63 return overlap(exon1.a, exon1.b, exon2.a, exon2.b); in canMerge()
/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/
H A Densexon.c3493 if (!exon1) in ensExonMatch()
3499 if (exon1 == exon2) in ensExonMatch()
3575 if (!exon1) in ensExonSimilarity()
3581 if (exon1 == exon2) in ensExonSimilarity()
3676 exon1, in listExonCompareEndAscending()
3682 if (exon1 && (!exon2)) in listExonCompareEndAscending()
3688 if ((!exon1) && exon2) in listExonCompareEndAscending()
3727 exon1, in listExonCompareEndDescending()
3778 exon1, in listExonCompareIdentifierAscending()
3835 exon1, in listExonCompareStartAscending()
[all …]
H A Densexon.h251 AjBool ensExonMatch(const EnsPExon exon1, const EnsPExon exon2);
253 AjBool ensExonSimilarity(const EnsPExon exon1, const EnsPExon exon2);
H A Densintron.c252 EnsPIntron ensIntronNewIni(EnsPExon exon1, in ensIntronNewIni() argument
279 exon1, in ensIntronNewIni()
283 ensExonTrace(exon1, 1); in ensIntronNewIni()
287 if (!exon1) in ensIntronNewIni()
293 feature1 = ensExonGetFeature(exon1); in ensIntronNewIni()
376 intron->PreviousExon = ensExonNewRef(exon1); in ensIntronNewIni()
H A Densintron.h69 EnsPIntron ensIntronNewIni(EnsPExon exon1,
H A Densgene.c2719 EnsPExon exon1 = *(EnsOExon *const *) item1; in listExonCompareAddressAscending() local
2727 exon1, in listExonCompareAddressAscending()
2731 if (ensExonSimilarity(exon1, exon2) == ajTrue) in listExonCompareAddressAscending()
2734 if (exon1 < exon2) in listExonCompareAddressAscending()
2737 if (exon1 > exon2) in listExonCompareAddressAscending()
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/__testing/
H A Dlongest_orfs.gff34 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p1.exon1;Parent=CUFF.38.1.p1
11 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p2.exon1;Parent=CUFF.38.1.p2
18 CUFF.38.1 transdecoder exon 1 7903 . - . ID=CUFF.38.1.p3.exon1;Parent=CUFF.38.1.p3
25 CUFF.38.1 transdecoder exon 1 7903 . - . ID=CUFF.38.1.p4.exon1;Parent=CUFF.38.1.p4
31 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p5.exon1;Parent=CUFF.38.1.p5
38 CUFF.24.1 transdecoder exon 1 2538 . + . ID=CUFF.24.1.p1.exon1;Parent=CUFF.24.1.p1
45 CUFF.35.1 transdecoder exon 1 1885 . + . ID=CUFF.35.1.p1.exon1;Parent=CUFF.35.1.p1
52 CUFF.17.1 transdecoder exon 1 1368 . + . ID=CUFF.17.1.p1.exon1;Parent=CUFF.17.1.p1
121 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1
169 CUFF.6.1 transdecoder exon 1 1717 . + . ID=CUFF.6.1.p1.exon1;Parent=CUFF.6.1.p1
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H A D__test.simplest.expected3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1
9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1
16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1
23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2
29 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1
35 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1
40 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1
47 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1
87 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1
148 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1
[all …]
H A D__test.single_best.expected3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1
9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1
16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1
23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1
29 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1
34 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1
41 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1
81 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1
136 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1
211 CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1.p1.exon1;Parent=CUFF.4.1.p1
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H A D__test.wBlastNPfam.expected3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1
9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1
16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1
23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2
29 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1
35 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1
40 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1
47 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1
87 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1
148 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1
[all …]
H A D__test.best_w_homology.expected3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1
9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1
16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1
23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2
28 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1
33 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1
40 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1
80 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1
135 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1
210 CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1.p1.exon1;Parent=CUFF.4.1.p1
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases_genbank/
H A Drw-451.gff33 scaffold_944 JAMg exon 32926 33084 . - . ID=J14826.1.exon1;Parent=J14826.1
8 scaffold_944 JAMg exon 32926 33084 . - . ID=J24826.1.exon1;Parent=J24826.1
13 scaffold_944 JAMg exon 32926 33084 . - . ID=J34826.1.exon1;Parent=J34826.1
H A Dmss-528.gff314 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
/dports/biology/py-gffutils/gffutils-0.10.1/gffutils/test/data/
H A Dgff_example1.gff36 … 4772649 4772814 . - . Name=ENSMUST00000045689.exon1;Parent=ENSMUST00000045689;ID=ENSMUST000000456…
/dports/biology/hyphy/hyphy-2.5.33/Examples/MoreComplexModels/
H A DExonIntron.bf47 DataSetFilter exon1 = CreateFilter (sequences,3,"0-98", "","TAA,TAG,TGA");
59 HarvestFrequencies (observedFreq1, exon1, 1, 1, 1);
132 LikelihoodFunction theLnLik = (exon1, exon1Tree,
/dports/biology/bedtools/bedtools2-2.30.0/test/intersect/
H A Dexons.issue750.bed1 chr1 0 100 exon1 1 +
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsuggadj.c229 static Int4 overlap_aas (struct match *exon1, struct match *exon2) in overlap_aas() argument
235 if ( exon1 -> p_pos >= exon2 -> p_pos){ in overlap_aas()
236 if ( exon1 -> p_pos <= (end2=exon2 -> p_pos +exon2 ->length -1) ){ in overlap_aas()
237 if ( (diff= exon1 -> p_pos - exon2 -> p_pos) > 0 ){ in overlap_aas()
244 if ( exon2 -> p_pos <= (end1=exon1 -> p_pos +exon1 ->length -1) ){ in overlap_aas()
255 retval, exon1 -> p_pos, exon1 -> length, in overlap_aas()
/dports/biology/primer3/primer3-2.3.6/test/
H A Dprimer_mispriming_input1 SEQUENCE_ID=exon1
H A Dprimer_mispriming_th_input7 SEQUENCE_ID=exon1
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_SeqIO_features.py231 exon1 = FeatureLocation(1148, 1188, strand=-1)
233 expected_loc = exon1 + exon2
241 exon1 = FeatureLocation(69610, 69724, strand=-1)
244 expected_loc = exon1 + exon2 + exon3
248 exon1 = FeatureLocation(69610, 69724, strand=+1)
251 expected_loc = exon1 + exon2 + exon3
255 exon1 = FeatureLocation(69610, 69724, strand=+1)
258 expected_loc = exon1 + exon2 + exon3
264 exon1 = FeatureLocation(69610, 69724, strand=-1)
267 expected_loc = exon1 + exon2 + exon3
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/
H A Dbest_placement.cpp289 const CSpliced_exon& exon1, in GetGapLengthOnRow()
293 const auto r1 = exon1.GetRowSeq_range(row, true); in GetGapLengthOnRow()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/
H A DDataProviderForExampleGencodeGtfGene.java46 final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); in createGencodeGtfGeneFeature() local
317 exon1.setUcscGenomeVersion(FuncotatorTestConstants.REFERENCE_VERSION_HG38); in createGencodeGtfGeneFeature()
356 exon1.setStartCodon(startCodon1); in createGencodeGtfGeneFeature()
362 transcript1.addExon(exon1); in createGencodeGtfGeneFeature()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/import/unit_test/data/input/
H A Dtest-multi-rna.gff314 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases/
H A Dmss-528.gff314 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/
H A DGencodeGtfCodecUnitTest.java188 final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); in createGencodeGtfGene_gencode_valid_gencode_file2() local
1131 exon1.setUcscGenomeVersion("hg38"); in createGencodeGtfGene_gencode_valid_gencode_file2()
1175 exon1.setCds(cds1); in createGencodeGtfGene_gencode_valid_gencode_file2()
1176 exon1.setStartCodon(start_codon1); in createGencodeGtfGene_gencode_valid_gencode_file2()
1190 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_valid_gencode_file2()
2189 exon1.setUcscGenomeVersion("hg38"); in createGencodeGtfGene_gencode_and_this_is_a_valid_one_too_table()
2253 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_and_this_is_a_valid_one_too_table()
2981 exon1.setUcscGenomeVersion("hg19"); in createGencodeGtfGene_gencode_v19_valid_gencode_file2()
3023 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_v19_valid_gencode_file2()
3263 exon1.setUcscGenomeVersion("hg19"); in createGencodeGtfGene_gencode_v19_and_this_is_a_valid_one_too()
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