/dports/math/SCIP/scip-7.0.3/applications/STP/check/testset/ |
H A D | GENE.test | 1 ../steinlib/GENE/gene181.stp 2 ../steinlib/GENE/gene1.stp 3 ../steinlib/GENE/gene425.stp 4 ../steinlib/GENE/gene4.stp 5 ../steinlib/GENE/gene442.stp 6 ../steinlib/GENE/gene575.stp 7 ../steinlib/GENE/gene602.stp 8 ../steinlib/GENE/gene61a.stp 9 ../steinlib/GENE/gene61b.stp 10 ../steinlib/GENE/gene61c.stp [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/example/ |
H A D | adeno_virus_b.gff | 1 NC_001405 NCBI cds 559 1542 . + . ID=cds.1;Alias=GENE:E1a,LocusTag:HAdVCgp01,GeneID:2652980;Dbxref=… 2 NC_001405 NCBI cds 559 1542 . + . ID=cds.2;Alias=GENE:E1a,LocusTag:HAdVCgp01,GeneID:2652980;Dbxref=… 3 NC_001405 NCBI cds 559 1315 . + . ID=cds.3;Alias=GENE:E1a,LocusTag:HAdVCgp01,GeneID:2652980;Dbxref=… 4 NC_001405 NCBI cds 1711 2238 . + . ID=cds.4;Alias=GENE:E1b_1,LocusTag:HAdVCgp02,GeneID:2652981;Dbxr… 6 NC_001405 NCBI cds 2016 3503 . + . ID=cds.6;Alias=GENE:E1b_1,LocusTag:HAdVCgp02,GeneID:2652981;Dbxr… 9 NC_001405 NCBI cds 4081 5708 . - . ID=cds.9;Alias=GENE:IVa2;Dbxref=NCBI_PID:NP_040515.1,NCBI_GI:962… 10 NC_001405 NCBI cds 5187 8357 . - . ID=cds.10;Alias=GENE:DNA polymerase;Dbxref=NCBI_PID:NP_040516.1,… 11 NC_001405 NCBI cds 7968 8417 . + . ID=cds.11;Alias=GENE:L1,LocusTag:HAdVCgp12,GeneID:2652993;Dbxref… 17 NC_001405 NCBI cds 15873 16469 . + . ID=cds.17;Alias=GENE:Pro-VII;Dbxref=NCBI_PID:NP_040522.1,NCBI_… 20 NC_001405 NCBI cds 18838 21744 . + . ID=cds.20;Alias=GENE:L4,LocusTag:HAdVCgp10,GeneID:2652998;Dbxr… [all …]
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/__testing/ |
H A D | longest_orfs.gff3 | 1 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p1;Name=ORF%20type%3Acomplete… 8 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p2;Name=ORF%20type%3Acomplete… 15 CUFF.38.1 transdecoder gene 1 7903 . - . ID=GENE.CUFF.38.1~~CUFF.38.1.p3;Name=ORF%20type%3Acomplete… 28 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p5;Name=ORF%20type%3Acomplete… 35 CUFF.24.1 transdecoder gene 1 2538 . + . ID=GENE.CUFF.24.1~~CUFF.24.1.p1;Name=ORF%20type%3Acomplete… 42 CUFF.35.1 transdecoder gene 1 1885 . + . ID=GENE.CUFF.35.1~~CUFF.35.1.p1;Name=ORF%20type%3Acomplete… 49 CUFF.17.1 transdecoder gene 1 1368 . + . ID=GENE.CUFF.17.1~~CUFF.17.1.p1;Name=ORF%20type%3Acomplete… 56 CUFF.49.1 transdecoder gene 1 2422 . - . ID=GENE.CUFF.49.1~~CUFF.49.1.p1;Name=ORF%20type%3Acomplete… 63 CUFF.49.1 transdecoder gene 1 2422 . + . ID=GENE.CUFF.49.1~~CUFF.49.1.p2;Name=ORF%20type%3Acomplete… 77 CUFF.45.1 transdecoder gene 1 4899 . - . ID=GENE.CUFF.45.1~~CUFF.45.1.p2;Name=ORF%20type%3Acomplete… [all …]
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H A D | __test.simplest.expected | 1 CUFF.1.1 transdecoder gene 1 503 . + . ID=GENE.CUFF.1.1~~CUFF.1.1.p1;Name=ORF%20type%3A5prime_parti… 7 CUFF.11.1 transdecoder gene 1 938 . + . ID=GENE.CUFF.11.1~~CUFF.11.1.p1;Name=ORF%20type%3A5prime_pa… 13 CUFF.12.1 transdecoder gene 1 2733 . + . ID=GENE.CUFF.12.1~~CUFF.12.1.p1;Name=ORF%20type%3Acomplete… 26 CUFF.13.1 transdecoder gene 1 1770 . + . ID=GENE.CUFF.13.1~~CUFF.13.1.p1;Name=ORF%20type%3Acomplete… 33 CUFF.13.2 transdecoder gene 1 875 . + . ID=GENE.CUFF.13.2~~CUFF.13.2.p1;Name=ORF%20type%3Ainternal%… 44 CUFF.14.1 transdecoder gene 1 1275 . + . ID=GENE.CUFF.14.1~~CUFF.14.1.p1;Name=ORF%20type%3Acomplete… 57 CUFF.16.1 transdecoder gene 1 1374 . + . ID=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=ORF%20type%3Acomplete… 64 CUFF.17.1 transdecoder gene 1 1368 . + . ID=GENE.CUFF.17.1~~CUFF.17.1.p1;Name=ORF%20type%3Acomplete… 84 CUFF.2.1 transdecoder gene 1 1060 . + . ID=GENE.CUFF.2.1~~CUFF.2.1.p1;Name=ORF%20type%3Acomplete%20… 131 CUFF.28.1 transdecoder gene 1 1584 . - . ID=GENE.CUFF.28.1~~CUFF.28.1.p1;Name=ORF%20type%3Acomplete… [all …]
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H A D | __test.single_best.expected | 1 CUFF.1.1 transdecoder gene 1 503 . + . ID=GENE.CUFF.1.1~~CUFF.1.1.p1;Name=ORF%20type%3A5prime_parti… 7 CUFF.11.1 transdecoder gene 1 938 . + . ID=GENE.CUFF.11.1~~CUFF.11.1.p1;Name=ORF%20type%3A5prime_pa… 13 CUFF.12.1 transdecoder gene 1 2733 . + . ID=GENE.CUFF.12.1~~CUFF.12.1.p1;Name=ORF%20type%3Acomplete… 20 CUFF.13.1 transdecoder gene 1 1770 . + . ID=GENE.CUFF.13.1~~CUFF.13.1.p1;Name=ORF%20type%3Acomplete… 27 CUFF.13.2 transdecoder gene 1 875 . + . ID=GENE.CUFF.13.2~~CUFF.13.2.p1;Name=ORF%20type%3Ainternal%… 38 CUFF.14.1 transdecoder gene 1 1275 . + . ID=GENE.CUFF.14.1~~CUFF.14.1.p1;Name=ORF%20type%3Acomplete… 51 CUFF.16.1 transdecoder gene 1 1374 . + . ID=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=ORF%20type%3Acomplete… 58 CUFF.17.1 transdecoder gene 1 1368 . + . ID=GENE.CUFF.17.1~~CUFF.17.1.p1;Name=ORF%20type%3Acomplete… 78 CUFF.2.1 transdecoder gene 1 1060 . + . ID=GENE.CUFF.2.1~~CUFF.2.1.p1;Name=ORF%20type%3Acomplete%20… 119 CUFF.28.1 transdecoder gene 1 1584 . - . ID=GENE.CUFF.28.1~~CUFF.28.1.p1;Name=ORF%20type%3Acomplete… [all …]
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H A D | __test.wBlastNPfam.expected | 1 CUFF.1.1 transdecoder gene 1 503 . + . ID=GENE.CUFF.1.1~~CUFF.1.1.p1;Name=ORF%20type%3A5prime_parti… 26 CUFF.13.1 transdecoder gene 1 1770 . + . ID=GENE.CUFF.13.1~~CUFF.13.1.p1;Name=ORF%20type%3Acomplete… 57 CUFF.16.1 transdecoder gene 1 1374 . + . ID=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=ORF%20type%3Acomplete… 58 CUFF.16.1 transdecoder mRNA 1 1374 . + . ID=CUFF.16.1.p1;Parent=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=O… 131 CUFF.28.1 transdecoder gene 1 1584 . - . ID=GENE.CUFF.28.1~~CUFF.28.1.p1;Name=ORF%20type%3Acomplete… 138 CUFF.29.1 transdecoder gene 1 1173 . + . ID=GENE.CUFF.29.1~~CUFF.29.1.p1;Name=ORF%20type%3Acomplete… 219 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p1;Name=ORF%20type%3Acomplete… 226 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p2;Name=ORF%20type%3Acomplete… 227 CUFF.38.1 transdecoder mRNA 1 7903 . + . ID=CUFF.38.1.p2;Parent=GENE.CUFF.38.1~~CUFF.38.1.p2;Name=O… 233 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p5;Name=ORF%20type%3Acomplete… [all …]
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H A D | __test.best_w_homology.expected | 1 CUFF.1.1 transdecoder gene 1 503 . + . ID=GENE.CUFF.1.1~~CUFF.1.1.p1;Name=ORF%20type%3A5prime_parti… 50 CUFF.16.1 transdecoder gene 1 1374 . + . ID=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=ORF%20type%3Acomplete… 51 CUFF.16.1 transdecoder mRNA 1 1374 . + . ID=CUFF.16.1.p1;Parent=GENE.CUFF.16.1~~CUFF.16.1.p1;Name=O… 118 CUFF.28.1 transdecoder gene 1 1584 . - . ID=GENE.CUFF.28.1~~CUFF.28.1.p1;Name=ORF%20type%3Acomplete… 119 CUFF.28.1 transdecoder mRNA 1 1584 . - . ID=CUFF.28.1.p1;Parent=GENE.CUFF.28.1~~CUFF.28.1.p1;Name=O… 125 CUFF.29.1 transdecoder gene 1 1173 . + . ID=GENE.CUFF.29.1~~CUFF.29.1.p1;Name=ORF%20type%3Acomplete… 126 CUFF.29.1 transdecoder mRNA 1 1173 . + . ID=CUFF.29.1.p1;Parent=GENE.CUFF.29.1~~CUFF.29.1.p1;Name=O… 193 CUFF.38.1 transdecoder gene 1 7903 . + . ID=GENE.CUFF.38.1~~CUFF.38.1.p1;Name=ORF%20type%3Acomplete… 194 CUFF.38.1 transdecoder mRNA 1 7903 . + . ID=CUFF.38.1.p1;Parent=GENE.CUFF.38.1~~CUFF.38.1.p1;Name=O… 207 CUFF.4.1 transdecoder gene 1 555 . + . ID=GENE.CUFF.4.1~~CUFF.4.1.p1;Name=ORF%20type%3A3prime_parti… [all …]
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/dports/biology/p5-Bio-Cluster/Bio-Cluster-1.7.3/lib/Bio/ClusterIO/ |
H A D | unigene.pm | 89 GENE => q/GENE\s+(\S.*)/, 169 $unigene{GENE} = $1; 259 $UGobj->gene($unigene{GENE}) if defined ($unigene{GENE});
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/ |
H A D | SnpEffUtil.java | 81 snpEffectGraph.put(EffectType.TRANSCRIPT,EffectType.GENE); in snpEffectGraph.put() argument 82 snpEffectGraph.put(EffectType.REGULATION,EffectType.GENE); in snpEffectGraph.put() argument 85 snpEffectGraph.put(EffectType.GENE,EffectType.CHROMOSOME); in snpEffectGraph.put() argument 164 GENE, enumConstant
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/dports/biology/jalview/jalview/src/jalview/ext/ensembl/ |
H A D | EnsemblSymbol.java | 45 private static final String GENE = "gene"; field in EnsemblSymbol 80 if (id != null && GENE.equals(type)) in parseSymbolResponse() 146 URL url = getUrl(query, taxon, GENE); in getGeneIds()
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/dports/biology/ugene/ugene-40.1/src/plugins/annotator/src/ |
H A D | CustomAutoAnnotationDialog.cpp | 53 genesBox->setChecked(!filteredFeatures.contains(PlasmidFeatureTypes::GENE)); in loadSettings() 68 filteredFeatures.append(PlasmidFeatureTypes::GENE); in saveSettings()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/stratifications/ |
H A D | SnpEffPositionModifier.java | 22 GENE, // EXON enumConstant 51 …f(effectType, SnpEffUtil.EffectType.EXON)) relevantStates.add(PositionModifier.GENE.name()); in getRelevantStates()
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/dports/graphics/xd3d/xd3d-8.3.1/src/graphic/ |
H A D | param.f | 10 CHARACTER*132 ABSC,ORDON,GENE variable 17 COMMON / CARAC / ABSC,ORDON,GENE,NOMPS,PROGEFF,LEGEND,FICHIER local
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/dports/biology/py-orange3-single-cell/orange3-single-cell-0.8.2/orangecontrib/single_cell/widgets/ |
H A D | owmarkergenes.py | 54 GENE = 1 variable in HeaderIndex 61 HeaderLabels = {HeaderIndex.GENE: 'Entrez ID', 330 if (model.index(row_index, HeaderIndex.GENE).data(), 349 gene_id = self.view.selectionModel().selectedRows(HeaderIndex.GENE) 361 output.attributes[GENE_ID_COLUMN] = HeaderLabels[HeaderIndex.GENE]
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/dports/biology/kallisto/kallisto-0.46.1/src/ |
H A D | GeneModel.cpp | 282 enum Type {GENE, TRANSCRIPT, EXON, OTHER}; in addGTFLine() enumerator 285 type = Type::GENE; in addGTFLine() 330 if (type == Type::GENE) { in addGTFLine() 378 if (type == Type::GENE) { in addGTFLine() 417 if (type == Type::GENE) { in addGTFLine()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/unit_test/data/ |
H A D | aa.129295 | 1 >gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/unit_test/data/ |
H A D | aa.129295 | 1 >gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/ |
H A D | AbstractGtfCodec.java | 149 if ((gene != null) && (featureType == GencodeGtfFeature.FeatureType.GENE)) { in decode() 184 case GENE: in decode() 408 if ( (featureType != GencodeGtfFeature.FeatureType.GENE) && in validateBaseGtfFeatureFields()
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/dports/biology/jalview/jalview/src/jalview/io/gff/ |
H A D | SequenceOntologyI.java | 64 public static final String GENE = "gene"; field
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/dports/biology/bbmap/bbmap/current/gff/ |
H A D | GbffFeature.java | 158 bb.append((pseudo && type==GENE) ? "pseudogene" : typeStringsGff[type]).tab(); in appendGff() 221 …public static final int GENE=0, CDS=1, rRNA=2, tRNA=3, ncRNA=4, repeat_region=5, UTR5=6, UTR3=7, i… field in GbffFeature
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/ |
H A D | SnpEffUtilUnitTest.java | 26 tests.add(new Object[]{SnpEffUtil.EffectType.GENE,SnpEffUtil.EffectType.CHROMOSOME}); in childParentpairs() 54 tests.add(new Object[]{SnpEffUtil.EffectType.GENE,SnpEffUtil.EffectType.NONE}); in nonchildParentpairs()
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/data/ |
H A D | xref.uniprot | 86 ZFIN ZDB-GENE-030131-6583; ywhaba 90 Xenbase XB-GENE-1006026; ywhab
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H A D | xref.embl | 58 ZFIN ZDB-GENE-000406-10
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/dports/biology/subread/subread-2.0.2-source/test/featureCounts/ |
H A D | test_commonusage.sh | 16 for level in GENE EXON
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/dports/biology/py-goatools/goatools-1.1.6/goatools/anno/ |
H A D | idtogos_reader.py | 27 prt.write('{GENE}\t{GOs}\n'.format(GENE=geneid, GOs=';'.join(sorted(goset))))
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