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DNA sequences batch blast against GO (fwd)

Steffen Hennig hennig at molgen.mpg.de
Fri Feb 6 04:23:26 PST 2004


Dear Jane,

at the MPI for Molecular Genetics in Berlin we are running a service
called GOblet ( http://goblet.molgen.mpg.de ), which is listed under
the GOA tools. We will come up with a new version in the next days
allowing batch processing of sequences (DNA or AA). Apart from the
web-service we are happy to process very large batches on  the basis
of a cooperation. So, interested people are welcome to contact us.

   best regards,
                 Steffen

On Fri, 6 Feb 2004, Jane Lomax wrote:

>
> ---------- Forwarded message ----------
> Date: Thu, 05 Feb 2004 09:29:17 -0600
> From: Xiaoping.Gou-1 <gouxping at ou.edu>
> To: go at genome.stanford.edu
> Subject: DNA sequences batch blast against GO
>
>
>
> Dear GO:
>
> I have more than 1000 ESTs now and I will have more than 10000 ESTs later. I want to annotate and classify them according to GeneOntology. The problem is, although I read almost all the documents on http://www.geneontology.org/, I still can't find a web tool that can be used to do batch DNA sequences query against GO. The AmiGo can be used to do blastX with only one sequence. Whould you please give me some suggestions?
>
> Usually I can convert a FASTA file to a database and BLAST against it locally. But, I just found the go_200401-seqdblite.fasta.gz file at http://www.godatabase.org/dev/database/archive/latest/, from which all IEA associations have been removed. Can I find a fasta file including the IEA assciations?
>
> I have Blasted the seqdblite.fasta and got some blast outputs. But,I am not a computer expert, it is difficulty for me to extract the GO IDs and find the corresponding GO terms to build an ontology of my own sequences. Could you please show me some septs?
>
> Regards,
> Xiaoping Gou
>
> -----------------------
> gouxping at ou.edu
>
>
>
>
>
> --
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>

==================================================================
        Dr.Steffen Hennig               Max-Planck-Institut
                                      fuer Molekulare Genetik
        Tel.+49-30-8413-1612              Ihnestr. 63/73
        Fax +49-30-8413-1380              D-14195 Berlin


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
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