<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sasha,<div><br></div><div>This gene model appears to be correctly formatted to me. In GFF3 format the CDS features are allowed to span multiple lines and they share the same ID to indicate that it is all the same features. See the GFF3 specification on the Sequence Ontology website (<a href="http://www.sequenceontology.org/resources/gff3.html">http://www.sequenceontology.org/resources/gff3.html</a>), and in particular the description of the ID attribute specifies:</div><div><br></div><blockquote class="webkit-indent-blockquote" style="margin: 0 0 0 40px; border: none; padding: 0px;"><div>ID Indicates the ID of the feature. IDs for each feature must be unique
within the scope of the GFF file. In the case of discontinuous
features (i.e. a single feature that exists over multiple genomic
locations) the same ID may appear on multiple lines. All lines that
share an ID collectively represent a single feature. </div></blockquote><div><span></span></div><div><br></div><div>So each of those CDS lines forms one part of the single CDS feature for this gene.</div><div><br></div><div>B</div><div> <br><div><div>On Mar 11, 2013, at 3:46 AM, Sasha Mikheyev wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div>Dear Yandell lab,</div><div><br></div><div>I am re-annotating the harvester and genome using protein and RNA-seq data. However, I get many artifacts like the one below. It seems that there are several CDS records that should tie in to the same mRNA, but they are really hanging out separately, and produce several nucleotide sequences with the same name when extracted from the gff. I would appreciate any guidance about how to fix this!</div>
<div><br></div><div>Thank you,</div><div><br></div><div>Sasha</div><div><br></div><div>grep "pbar_scf7180000350377:hit:2506" Pbar.2.0.gff </div><div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>protein2genome<span class="Apple-tab-span" style="white-space:pre"> </span>protein_match<span class="Apple-tab-span" style="white-space:pre"> </span>172004<span class="Apple-tab-span" style="white-space:pre"> </span>172162<span class="Apple-tab-span" style="white-space:pre"> </span>150<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;score=150;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>protein2genome<span class="Apple-tab-span" style="white-space:pre"> </span>match_part<span class="Apple-tab-span" style="white-space:pre"> </span>172004<span class="Apple-tab-span" style="white-space:pre"> </span>172162<span class="Apple-tab-span" style="white-space:pre"> </span>150<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hsp:2798;Parent=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;Target=Hsal|HS9704 1 53 +;Gap=M159;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>mRNA<span class="Apple-tab-span" style="white-space:pre"> </span>538308<span class="Apple-tab-span" style="white-space:pre"> </span>558769<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506;Parent=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29;Name=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29-mRNA-1;_AED=0.48;_eAED=0.39;_QI=0|0|0|0.5|1|1|6|0|395;score=0.01;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>538308<span class="Apple-tab-span" style="white-space:pre"> </span>538334<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:305;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>538748<span class="Apple-tab-span" style="white-space:pre"> </span>538968<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:306;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>539842<span class="Apple-tab-span" style="white-space:pre"> </span>540242<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:307;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>542624<span class="Apple-tab-span" style="white-space:pre"> </span>542798<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:308;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>555823<span class="Apple-tab-span" style="white-space:pre"> </span>556025<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:309;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>558609<span class="Apple-tab-span" style="white-space:pre"> </span>558769<span class="Apple-tab-span" style="white-space:pre"> </span>0.01<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:exon:310;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>538308<span class="Apple-tab-span" style="white-space:pre"> </span>538334<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:305;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>538748<span class="Apple-tab-span" style="white-space:pre"> </span>538968<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>0<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:306;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>539842<span class="Apple-tab-span" style="white-space:pre"> </span>540242<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:307;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>542624<span class="Apple-tab-span" style="white-space:pre"> </span>542798<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:308;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>555823<span class="Apple-tab-span" style="white-space:pre"> </span>556025<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:309;Parent=pbar_scf7180000350377:hit:2506;</div>
<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>558609<span class="Apple-tab-span" style="white-space:pre"> </span>558769<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>ID=pbar_scf7180000350377:hit:2506:cds:310;Parent=pbar_scf7180000350377:hit:2506;</div>
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<div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div><br class="Apple-interchange-newline">
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