[Bioperl-l] EST functional categories
Joshua A Udall
jaudall at iastate.edu
Tue Jan 27 12:43:15 EST 2004
At 02:57 PM 1/25/2004, Eckhard Lehmann wrote:
> > I'm working on an EST project. I'd like to use bioperl to identify
> > putative functional categories of individual ESTs and eventually end up
> > with those ubiquitous pie charts or histograms (using excel). I've seen
> > that ontologies structures have been built into bioperl but there isn't
> > much documentation (or I've overlooked it). I could use some help/example
>I am not quite sure about that - but isn't it better to do functional
>analysis on contigs that are assembled of EST's, rather that individual EST's?
Of course contigs, my mistake in the description.
> > scripts to get started. I've blasted all my ESTs against nr. How do I
> > take the best blast hit and look it it's functional category on
> > GO/Interpro?
>In the EST project that I am working on - I have the impression yet, that
>you can not pull out much usefull information of these short sequence parts.
>When it comes to BLASTx for instance, you get many many different
>discusting non-informative hits.
>With contigs you have mostly eliminated the redundancy and can do better
>BLASTx. Functional analysis should then be possible by backtracking the EST
sure, and even more confusing is that I'm working with a polyploid. You're
right the contigs help a lot but assuming I want to use the best blast hit,
how do I retrieve a GO object using that Arabidopsis gene id (from nr)?
>I have done some stuff, but it is mainly database oriented (PostgreSQL,
>PL/PgSQL) and has not much to do with BioPerl currently. Used only
>load the EST sequences into a BioSQL setup along with contigs and things, and
>now to fetch individual sequences into flat files sometimes.
>However, I used Perl and GD::Graph for making pie charts and a web interface
>to the database.
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>Bioperl-l at portal.open-bio.org
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
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