[maker-devel] Moving Annotation to New Assembly

[Carson Holt]

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.

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.

—Carson

> On Jan 8, 2016, at 8:05 AM, Shaw, Sophie <s.shaw at abdn.ac.uk> wrote:
> 
> Dear Maker Team,
> 
> 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 - https://groups.google.com/forum/#!searchin/maker-devel/est_forward/maker-devel/q9fxXGKO8mk/0ATwhJvZeI4J <https://groups.google.com/forum/#!searchin/maker-devel/est_forward/maker-devel/q9fxXGKO8mk/0ATwhJvZeI4J>
> 
> However all of the information in the final column of the GFF has not been transferred over, just the gene name. For example:
> 
> The original annotation is as follows:
> scaffold_252 maker
> gene 3018
> 4307 .
> + .
> 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;
> 
> And the new annotation after running MAKER with est_forward=1:
> scaffold_21 maker
> gene 18116
> 19405 .
> - .
> ID=maker-scaffold_21-exonerate_est2genome-gene-0.25;Name=CAUR_05562-RA-gene
> 
> 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.
> 
> All the Best,
> 
> Sophie Shaw
> 
> —
> Dr. Sophie Shaw 
> Bioinformatician 
> Centre for Genome Enabled Biology and Medicine
> University of Aberdeen
> 23 St. Machar Drive
> Old Aberdeen
> AB24 3RY
> https://www.abdn.ac.uk/genomics/ <https://www.abdn.ac.uk/genomics/> 
> 
> 
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160114/8fb0d67e/attachment-0003.html>