[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 
>confusing and
>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
>source information.

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 
>BioPerl-DB to
>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.
>Eckhard ;)
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Joshua Udall
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
Ames, IA 50011
Ph: (515) 294-7098
Fax: (515) 294-1337 

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