Bioperl: Re: BioPerl for transcriptional profiling

[Chris Dagdigian]

Dr. Ebbole --

I'm CC'ing this reply to the general bioperl discussion list
as there may be people there who have done similar work
or may even be at your University and will be better positioned
with advice...

The best (short) answer I have for you is that yes the BioPerl
codebase may be helpful to your project but it is not in a form
that would be useful right out of the 'box' to a non-perl user
or programmer. Generally speaking our software has been used
most successfully by sites that have programmers who are able to
take bioperl code and modules and integrate it into systems they are
building themselves. 

What you are trying to do seems fairly straightforward -- aligning some
ESTs to create contigs and then BLASTing them repeatedly looking
for new homologies. There may be commercial or free software out
there that can already do all (or 90%) of these things for you without needing 
a resident stable of bioinformaticians or programmers...perhaps others
on this list can make additional suggestions.

Regards,
Chris 


>>> "Dr. Daniel Ebbole" <d-ebbole@tamu.edu> 09/11 11:47 AM >>>
Hello, I was browsing through the list of participants of BioPerl and
found your interest in high throughput cDNA sequence analysis. I know
nothing about the specifics of Perl. We are a little shorthanded on
bioinformatics people here at the moment.  I work with Neurospora crassa
and about 10,000 cDNA sequences are available in GenBank.  The
sequencers who put the data there have limited resources/ability to
analyze this data sufficiently.  I would like to organize the data to
facilitate transcriptional profiling efforts.  The things I would like
to do is sort all the ESTs into their overlapping sets (defining a
minimal set of EST sequences for profiling) and make contigs to create
files for frequent BLASTing for homology searches for unknown genes.  Is
Perl/BioPerl something I should be looking into to help me accomplish
this?
Dan 
-- 
Daniel Ebbole
Associate Professor 
Program for the Biology of Filamentous Fungi 
Dept of Plant Pathology and Microbiology 
Texas A&M University
College Station, TX 77843-2132
USA 
Ph.409-845-4831 
Fax.409-845-6483

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