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E.coli annotations?

Daniel Barrell dbarrell at ebi.ac.uk
Mon Sep 19 01:09:23 PDT 2005


Hi Ian,

You may also find the GOA UniProt Proteome sets of use:

http://www.ebi.ac.uk/GOA/proteomes.html

These are subsets of the GOA UniProt annotations and cover  	Escherichia 
coli and Bacillus subtilis.

Cheers

Dan

Ian Holmes wrote:
> Hi Scot, this would be great. Can you tell me where I could find these
> annotations, either as a flatfile or AmiGO interface (or preferably both)?
> 
> I'm not focussing on any one species per se, but I'd probably begin with
> E.coli and B.subtilis. "Meaningful" is indeed ambiguous, but basically I
> am looking for robust (i.e. widely-implemented, relatively
> uncontroversial) functional annotations, suitable for demonstration and
> simple investigations. So, for example, I'm interested in metabolism &
> biosynthesis, with a view to prediction of auxotrophic characteristics.
> The broader the scope of the annotations, the better. Any pointers or help
> you can give would be wonderful.
> 
> Thanks..
> Ian
> 
> On Sun, 18 Sep 2005, Scot E. Dowd Ph.D. wrote:
> 
> 
>>Hi Ian,
>>We currently have GO annotations for all fully sequenced bacterial genomes.
>>Our site is being refabricated over the next week so links are not
>>activated, but feel free to contact me with your needs.
>>E.g. if you are looking for a dedicated AmiGO site with Ecoli GO etc.
>>
>>Of course your definition of meaningful will always play a role in anyones
>>ability to provide such.
>>
>>SED
>>
>>Liru.ars.usda.gov/mainbioinformatics.html
>>
>>
>>
>>>-----Original Message-----
>>>From: owner-gofriends at genome.stanford.edu
>>>[mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Ian Holmes
>>>Sent: Sunday, September 18, 2005 12:55 AM
>>>To: gofriends at genome.stanford.edu
>>>Subject: E.coli annotations?
>>>
>>>Hi all
>>>
>>>I'm currently teaching an introductory class in compbio &
>>>naturally would like to discuss GO. Since microbial
>>>annotation will feature in the class, I had thought to use
>>>carbohydrate metabolism in E.coli as an initial example.
>>>However I have, so far, been unable to find meaningful GO
>>>annotations of E.coli (though E.coli is listed on the AmiGO
>>>website and by various GO affiliates) .  My question: where
>>>are the E.coli annotations?
>>>Or is something like EcoCyc the only option for this
>>>organism?  And if the latter, what is the prokaryotic
>>>coverage, and to what extent can GO currently be used as a
>>>prokaryotic annotation resource?
>>>
>>>yours hopefully
>>>Ian
>>>
>>>--
>>>This message is from the GOFriends moderated mailing list.  A
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>>
>>
>>--
>>This message is from the GOFriends moderated mailing list.  A list of public
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> 
> 
> 
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
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-- 

Daniel Barrell
EMBL - The EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone: +44 (0)1223 492551
Email: dbarrell at ebi.ac.uk

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