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[gofriends] Re: Fwd: Web tool to replace GOFigure?

Stefan Goetz sgoetz at cipf.es
Mon Dec 17 06:33:22 PST 2007


Dear Alexander, Kimberly and GO-Community,
Go-Figure is a tool for Gene Ontology annotation based on BLAST. 
GoFigure maps GO terms to BLAST hits by minimum covering graph 
construction. Blast2GO generates/predicts GO annotations based on BLAST 
results considering the of the GO DAG structure plus GO Evidence Codes 
and all BLAST Hit similarities. (FASTA files as Input) 
Blast2GO is high-throughput capable and the Web-Start version, free 
available at www.blast2go.org, runs fine for 40.000 sequences (or more 
-> memory dependent ). Alexander, you are most welcome to write us for 
more details.

We are right now implementing a full configurable, high-throughput, web 
version of Blast2GO which will be available in 2 to 3 weeks at 
http://babelomics.bioinfo.cipf.es. We will announce the release of 
Blast2GO-WEB on this list.

Kimberly, I think it would be of great value to a lot of users who are 
working with novel or uncharacterised sequences/proteins to add a 
functional annotation feature based on BLAST directly to the Amigo 
website and Blast2GO would definitely be a solid option. In case you are 
considering this we would be very pleased to hear from you.

Best regards,
Stefan Goetz



Kimberly Van Auken wrote:
> Dear Alexander,
>
> Thanks for writing toDear Alexander,
>
> Thanks for writing to the GO.
>
> I'm forwarding your query on to the gofriends mailing list to see if 
> anyone
> is aware of a tool like GOFigure where you can choose the GO category you
> want returned prior to running a batch search with FASTA files.
>
> This may be a feature we could consider adding to the BLAST search on 
> the AmiGO site.
>
> Regards,
> Kimberly Van the GO.
>
> I'm forwarding your query on to the gofriends mailing list to see if 
> anyone
> is aware of a tool like GOFigure where you can choose the GO category you
> want returned prior to running a batch search with FASTA files.
>
> This may be a feature we could consider adding to the BLAST search on 
> the AmiGO site.
>
> Regards,
> Kimberly Van Auken
>
> Database Curator, WormBase
> www.wormbase.org
> www.geneontology.org
>
>
>
>> Date: Wed, 12 Dec 2007 05:22:57 -0800 (PST)
>> Message-Id: <200712121322.FAA19483 at bread.Stanford.EDU 
>> <mailto:200712121322.FAA19483 at bread.Stanford.EDU>>
>> To: witeka at uni-mainz.de <mailto:witeka at uni-mainz.de>
>> Subject: GO Help query (from website)
>> From: noreply at genome.stanford.edu <mailto:noreply at genome.stanford.edu>
>>
>> contactName: Alexander Witek
>> contactEmail: witeka at uni-mainz.de <mailto:witeka at uni-mainz.de>
>> contactText: Dear colleagues,
>>
>> i´m searching for a web-based gene ontology annotation toll like 
>> GOfigure (wich is not available any more), where i can put in batch 
>> jobs with fasta format sequences and where i can choose before 
>> starting the job wich GO category i would like to prefer.
>>
>> Can you help me with that?
>>
>> Best wishes
>>
>> Alexander Witek
>>
>
>
> -- 
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>


-- 

--------------------------------------------
Stefan Götz
Bioinformatics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------


--
This message is from the GOFriends moderated mailing list.  A list of public
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