[maker-devel] Functional annotation pipeline

[Shane Brubaker]

Great thank you ... I will take a look at those.

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Friday, April 13, 2012 2:03 PM
To: Joseph Fass; Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Functional annotation pipeline

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files.  There are also a couple of scripts maker_functional_gff and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From: Joseph Fass <joseph.fass at gmail.com<mailto:joseph.fass at gmail.com>>
Date: Fri, 13 Apr 2012 13:42:51 -0700
To: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>> wrote:
Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane

_______________________________________________
maker-devel mailing list
maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com<http://gmail.com> (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto: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/20120413/5437043b/attachment-0003.html>