[maker-devel] Functional annotation pipeline

[Carson Holt]

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>
Date:  Fri, 13 Apr 2012 13:42:51 -0700
To:  Shane Brubaker <sbrubaker at solazyme.com>
Cc:  "maker-devel at yandell-lab.org" <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>
wrote:
> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
> 
> Thanks,
> Shane
> 
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-- 
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)

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