<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">We do not have a tool that will copy over attributes from one GFF3 file to another based off of ID match. Your needs are specific enough that you may have to write a script yourself to copy the attributes you care about.</div><div class=""><br class=""></div><div class="">Truthfully I would recommend rerunning interproscan and blastp against swiss-prot, as these could probably use an update as anyways. The est_forward tool used to pull IDs forward is based solely off of alignment (they will not all be exact matches or complete matches - just best matches), so you cannot guarantee that all domain content will be completely identical. Interpro and swiss-prot also get periodically updated, so running these against the most recent releases can give more functional info. The purist in me would be inclined to redo the interproscn analysis and blastp against swiss-prot. Then you can use the maker_functional_gff, ipr_update_gff, and iprscan2gff3 scripts to properly add everything back in a way similar to the previous annotations.</div><div class=""><br class=""><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jan 8, 2016, at 8:05 AM, Shaw, Sophie <<a href="mailto:s.shaw@abdn.ac.uk" class="">s.shaw@abdn.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Dear Maker Team,</div>
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<div class="">I have reassembled some data that was previously assembled with different software and then annotated using MAKER. I want to transfer the MAKER annotation to the new fasta file. I’ve followed the instructions in the post here - <a href="https://groups.google.com/forum/#!searchin/maker-devel/est_forward/maker-devel/q9fxXGKO8mk/0ATwhJvZeI4J" class="">https://groups.google.com/forum/#!searchin/maker-devel/est_forward/maker-devel/q9fxXGKO8mk/0ATwhJvZeI4J</a></div>
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<div class="">However all of the information in the final column of the GFF has not been transferred over, just the gene name. For example:</div>
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<div class="">The original annotation is as follows:</div>
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<div class="">scaffold_252<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">
</span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>3018<span class="Apple-tab-span" style="white-space:pre">
</span>4307<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=CAUR_05562;Name=CAUR_05562;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to VHS1: Serine/threonine-protein kinase VHS1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c));Dbxref=Gene3D:G3DSA:1.10.510.10,Gene3D:G3DSA:3.30.200.20,InterPro:IPR000719,InterPro:IPR002290,InterPro:IPR008271,InterPro:IPR011009,InterPro:IPR017441,PANTHER:PTHR24343,PANTHER:PTHR24343:SF90,Pfam:PF00069,ProSitePatterns:PS00107,ProSitePatterns:PS00108,ProSiteProfiles:PS50011,SMART:SM00220,SUPERFAMILY:SSF56112;Ontology_term=GO:0004672,GO:0005524,GO:0006468,GO:0016772;</div>
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<div class="">And the new annotation after running MAKER with est_forward=1:</div>
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<div class="">scaffold_21<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">
</span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>18116<span class="Apple-tab-span" style="white-space:pre">
</span>19405<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=maker-scaffold_21-exonerate_est2genome-gene-0.25;Name=CAUR_05562-RA-gene</div>
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<div class="">Is there a way of pulling the Note part of the gff file over as well as the gene name (and is this even a correct thing to do - should I be re-running MAKER entirely?). The researchers don’t want to lose the information gained from the work on the previous
annotation.</div>
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<div class="">All the Best,</div>
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<div class="">Sophie Shaw</div>
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<div class="">—</div>
<div class="">Dr. Sophie Shaw </div>
<div class="">Bioinformatician </div>
<div class="">Centre for Genome Enabled Biology and Medicine</div>
<div class="">University of Aberdeen</div>
<div class="">23 St. Machar Drive</div>
<div class="">Old Aberdeen</div>
<div class="">AB24 3RY</div>
<div class=""><a href="https://www.abdn.ac.uk/genomics/" class="">https://www.abdn.ac.uk/genomics/</a> </div>
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The University of Aberdeen is a charity registered in Scotland, No SC013683.<br class="">
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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