[maker-devel] Functional annotation pipeline

[Daniel Hughes]

sorry, that's the new version of course.

dan.

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


2012/4/13 Daniel Hughes <dsth at ebi.ac.uk>

> 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)
>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>
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>
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