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annotate test-data/ecoli-k12.processed.gff3 @ 3:29769f789b8f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
author devteam
date Tue, 01 Oct 2019 12:19:52 -0400
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children 0cf496c45054
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3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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1 # gffread /home/hxr/arbeit/galaxy/database/files/000/dataset_791.dat -F -D -E -o output.gff3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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2 ##gff-version 3
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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3 NC_000913.3 RefSeq gene 190 255 . + . ID=gene-b0001;geneID=gene-b0001;gene_name=thrL;Dbxref=ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0001;locus_tag=b0001;protein_id=NP_414542.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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4 NC_000913.3 RefSeq CDS 190 255 . + 0 Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;locus_tag=b0001;orig_transcript_id=gnl|b0001|mrna.b0001;product=thr operon leader peptide;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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5 NC_000913.3 RefSeq gene 337 2799 . + . ID=gene-b0002;geneID=gene-b0002;gene_name=thrA;Dbxref=ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,thrA1,thrA2,thrD;locus_tag=b0002;protein_id=NP_414543.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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6 NC_000913.3 RefSeq CDS 337 2799 . + 0 Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;locus_tag=b0002;orig_transcript_id=gnl|b0002|mrna.b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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7 NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene-b0003;geneID=gene-b0003;gene_name=thrB;Dbxref=ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0003;locus_tag=b0003;protein_id=NP_414544.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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8 NC_000913.3 RefSeq CDS 2801 3733 . + 0 Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;locus_tag=b0003;orig_transcript_id=gnl|b0003|mrna.b0003;product=homoserine kinase;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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9 NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene-b0004;geneID=gene-b0004;gene_name=thrC;Dbxref=ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0004;locus_tag=b0004;protein_id=NP_414545.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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10 NC_000913.3 RefSeq CDS 3734 5020 . + 0 Parent=gene-b0004;Dbxref=UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;gbkey=CDS;locus_tag=b0004;orig_transcript_id=gnl|b0004|mrna.b0004;product=threonine synthase;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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11 NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene-b0005;geneID=gene-b0005;gene_name=yaaX;Dbxref=ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0005;locus_tag=b0005;protein_id=NP_414546.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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12 NC_000913.3 RefSeq CDS 5234 5530 . + 0 Parent=gene-b0005;Dbxref=UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,ASAP:ABE-0000015,ECOCYC:G6081,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;locus_tag=b0005;orig_transcript_id=gnl|b0005|mrna.b0005;product=DUF2502 domain-containing protein YaaX;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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13 NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene-b0006;geneID=gene-b0006;gene_name=yaaA;Dbxref=ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0006;locus_tag=b0006;protein_id=NP_414547.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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14 NC_000913.3 RefSeq CDS 5683 6459 . - 0 Parent=gene-b0006;Dbxref=UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,ASAP:ABE-0000018,ECOCYC:EG10011,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;locus_tag=b0006;orig_transcript_id=gnl|b0006|mrna.b0006;product=peroxide stress resistance protein YaaA;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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15 NC_000913.3 RefSeq gene 6529 7959 . - . ID=gene-b0007;geneID=gene-b0007;gene_name=yaaJ;Dbxref=ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=yaaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0007;locus_tag=b0007;protein_id=NP_414548.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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16 NC_000913.3 RefSeq CDS 6529 7959 . - 0 Parent=gene-b0007;Dbxref=UniProtKB/Swiss-Prot:P30143,Genbank:NP_414548.1,ASAP:ABE-0000020,ECOCYC:EG11555,EcoGene:EG11555,GeneID:944745;Name=NP_414548.1;gbkey=CDS;locus_tag=b0007;orig_transcript_id=gnl|b0007|mrna.b0007;product=putative transporter YaaJ;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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17 NC_000913.3 RefSeq gene 8238 9191 . + . ID=gene-b0008;geneID=gene-b0008;gene_name=talB;Dbxref=ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=talB;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0008,yaaK;locus_tag=b0008;protein_id=NP_414549.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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18 NC_000913.3 RefSeq CDS 8238 9191 . + 0 Parent=gene-b0008;Dbxref=UniProtKB/Swiss-Prot:P0A870,Genbank:NP_414549.1,ASAP:ABE-0000027,ECOCYC:EG11556,EcoGene:EG11556,GeneID:944748;Name=NP_414549.1;gbkey=CDS;locus_tag=b0008;orig_transcript_id=gnl|b0008|mrna.b0008;product=transaldolase B;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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19 NC_000913.3 RefSeq gene 9306 9893 . + . ID=gene-b0009;geneID=gene-b0009;gene_name=mog;Dbxref=ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=mog;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=bisD,chlG,ECK0009,mogA,yaaG;locus_tag=b0009;protein_id=NP_414550.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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20 NC_000913.3 RefSeq CDS 9306 9893 . + 0 Parent=gene-b0009;Dbxref=UniProtKB/Swiss-Prot:P0AF03,Genbank:NP_414550.1,ASAP:ABE-0000030,ECOCYC:EG11511,EcoGene:EG11511,GeneID:944760;Name=NP_414550.1;gbkey=CDS;locus_tag=b0009;orig_transcript_id=gnl|b0009|mrna.b0009;product=molybdopterin adenylyltransferase;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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21 NC_000913.3 RefSeq gene 9928 10494 . - . ID=gene-b0010;geneID=gene-b0010;gene_name=satP;Dbxref=ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=satP;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0010,yaaH;locus_tag=b0010;protein_id=NP_414551.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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22 NC_000913.3 RefSeq CDS 9928 10494 . - 0 Parent=gene-b0010;Dbxref=UniProtKB/Swiss-Prot:P0AC98,Genbank:NP_414551.1,ASAP:ABE-0000032,ECOCYC:EG11512,EcoGene:EG11512,GeneID:944792;Name=NP_414551.1;gbkey=CDS;locus_tag=b0010;orig_transcript_id=gnl|b0010|mrna.b0010;product=acetate/succinate:H(+) symporter;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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23 NC_000913.3 RefSeq gene 10643 11356 . - . ID=gene-b0011;geneID=gene-b0011;gene_name=yaaW;Dbxref=ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=yaaW;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0011;locus_tag=b0011;protein_id=NP_414552.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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24 NC_000913.3 RefSeq CDS 10643 11356 . - 0 Parent=gene-b0011;Dbxref=UniProtKB/Swiss-Prot:P75617,Genbank:NP_414552.1,ASAP:ABE-0000037,ECOCYC:G6082,EcoGene:EG14340,GeneID:944771;Name=NP_414552.1;gbkey=CDS;locus_tag=b0011;orig_transcript_id=gnl|b0011|mrna.b0011;product=putative enzyme-specific chaperone YaaW;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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25 NC_000913.3 RefSeq gene 10830 11315 . + . ID=gene-b0012;geneID=gene-b0012;gene_name=mbiA;Dbxref=ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=mbiA;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0012,htgA,htpY;locus_tag=b0012;protein_id=YP_009518733.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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26 NC_000913.3 RefSeq CDS 10830 11315 . + 0 Parent=gene-b0012;Dbxref=UniProtKB/Swiss-Prot:P28697,Genbank:YP_009518733.1,ASAP:ABE-0000040,ECOCYC:EG11509,EcoGene:EG11509,GeneID:948295;Name=YP_009518733.1;gbkey=CDS;locus_tag=b0012;orig_transcript_id=gnl|b0012|mrna.CDS13;product=uncharacterized protein MbiA;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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27 NC_000913.3 RefSeq gene 11382 11786 . - . ID=gene-b0013;geneID=gene-b0013;gene_name=yaaI;Dbxref=ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=yaaI;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0013;locus_tag=b0013;protein_id=NP_414554.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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28 NC_000913.3 RefSeq CDS 11382 11786 . - 0 Parent=gene-b0013;Dbxref=UniProtKB/Swiss-Prot:P28696,Genbank:NP_414554.1,ASAP:ABE-0000043,ECOCYC:G8202,EcoGene:EG11513,GeneID:944751;Name=NP_414554.1;gbkey=CDS;locus_tag=b0013;orig_transcript_id=gnl|b0013|mrna.b0013;product=DUF2541 domain-containing protein YaaI;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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29 NC_000913.3 RefSeq gene 12163 14079 . + . ID=gene-b0014;geneID=gene-b0014;gene_name=dnaK;Dbxref=ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=dnaK;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0014,groPAB,groPC,groPF,grpC,grpF,seg;locus_tag=b0014;protein_id=NP_414555.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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30 NC_000913.3 RefSeq CDS 12163 14079 . + 0 Parent=gene-b0014;Dbxref=UniProtKB/Swiss-Prot:P0A6Y8,Genbank:NP_414555.1,ASAP:ABE-0000052,ECOCYC:EG10241,EcoGene:EG10241,GeneID:944750;Name=NP_414555.1;gbkey=CDS;locus_tag=b0014;orig_transcript_id=gnl|b0014|mrna.b0014;product=chaperone protein DnaK;transl_table=11
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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31 NC_000913.3 RefSeq gene 14168 15298 . + . ID=gene-b0015;geneID=gene-b0015;gene_name=dnaJ;Dbxref=ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=dnaJ;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=ECK0015,groP,grpC;locus_tag=b0015;protein_id=NP_414556.1
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
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32 NC_000913.3 RefSeq CDS 14168 15298 . + 0 Parent=gene-b0015;Dbxref=UniProtKB/Swiss-Prot:P08622,Genbank:NP_414556.1,ASAP:ABE-0000054,ECOCYC:EG10240,EcoGene:EG10240,GeneID:944753;Name=NP_414556.1;gbkey=CDS;locus_tag=b0015;orig_transcript_id=gnl|b0015|mrna.b0015;product=chaperone protein DnaJ;transl_table=11