[maker-devel] Functional annotation pipeline

[Daniel Hughes]

Careful of interproscan atm.. I believe the executable is still in beta and
they definitely aren't recommending it for production use yet. If you do
use it be sure to check output file if using the lookup service as when i
used it recently it would sometimes exit normally despite lookup failures
(the lookup problems may have had something to do with running ~800 in
parallel - they're looking into the issue atm.).

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Carson Holt <carsonhh at gmail.com>

> 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 (professional)
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>
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