[Bioperl-l] New to BioPerl

[Jason Stajich]

use Bio::SearchIO and read the bptutorial on how to extract the
information you need -- all the tools you need to do this are in the
Bio::SearchIO parser system and Bio::Search objects.

I have a script that extracts tissue information for an EST
blast see scripts/est_tissue_query.pl in the bioperl repository.  That
script is trying to do a lot so it might be a little confusing.
it's run like
% perl scripts/est_tissue_query.pl -r genbank -p 0.00001 -f blast -b
MYFILE
# you can add -c cache if you want to build a temporary cache so multiple

This script has been fixed some just now to use Bio::SearchIO so you
probably want the latest CVS version which you can see how to get from
http://cvs.bioperl.org

I'd suggest that you spend a little time learning bioperl by running
through the tutorial and building a simle script that prints out the list
of hits from a blast report using our objects.  Then I suspect the path
will be more obvious.  Lots of good discussions of this type on our
mailing list archives.

-jason

On Wed, 27 Feb 2002 holford.5@osu.edu wrote:

> Does a Perl script exist for such a job or would I need to develop one?
>
> I am in the process of learning Perl and still very wet behind the ears.  I
> am a C/C++ programmer and I have been asked to develop a software program
> to automate a process.  This process deals with parsing blast
> output.  Since my background in not in Biology I will not attempt to
> paraphrase the request.  So here it is in its entirety.
>
> "Do you know of a program that would allow or facilitate in silico
>  > Northern (gene expression) analysis? What I would like to do is to take
>  > a specific gene sequence and blast it against the soybean EST database
>  > and then extract the hits below a certain E value into *categories*
>  > (e.g., "roots", "inoculated", etc) based on the cDNA library
>  > information for the particular EST in the text that accompanies the
>  > blast output. It could also be done based on the cDNA library #
>  > associated with the EST hits. This allows a quick determination of
>  > whether a particular gene, for instance, is root specific in its
>  > expression, etc. It would be extremely valuable to us in deciding what
>  > genes to focus on (from a gene family, for instance) for expression
>  > analysis with real life Northerns.
>  > I think that such a program would be very valuable for alot of us!"
>
> Thanking you in advance,
>
> Ian
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu