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E.coli annotations?

Ian Holmes ihh at bdgp.lbl.gov
Mon Nov 7 12:15:19 PST 2005


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:
http://biowiki.org/UsingGeneOntologyForBacterialAnnotation

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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