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ihh at bdgp.lbl.gov
Mon Nov 7 12:16:42 PST 2005
PS feel free to edit that wiki page if you have more up-to-date info!
On Mon, 7 Nov 2005, Ian Holmes wrote:
> hello Goers
> as a followup to my earlier question about prokaryote annotations (below)
> and your helpful responses, I'm attaching the throwaway Perl script I
> knocked up that retrieves, in FASTA format, the subset of UniProt
> descended from (i) a given GO term and (ii) a given NCBI taxonomic root.
> It requires several other files to work (basically the NCBI taxonomy
> database, the Gene Ontology OBO flatfile & the Uniprot associations).
> I am sure you all have far fancier tools for doing this sort of thing, but
> I thought it might nevertheless be of some use because (1) it's simple and
> self-contained; (2) it allows you to get taxon-specific stuff, e.g. for
> bacteria (which I wanted); and (3) the file "go_200510-seqdb.fasta.gz"
> that I got from the GO FTP site, which is supposed to contain the actual
> sequences, was missing quite a few that were in the assocations file.
> For reference, here also is a summary of the replies that you kindly sent
> to my earlier email:
> BTW I also have a script that does a similar thing for Pfam models, but
> I'm not inclined to post it, mainly because it exposes my increasingly
> embarrassing aversion to SQL.
> Best, Ian
> On Sat, 17 Sep 2005, Ian Holmes wrote:
> > 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
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