[Bioperl-l] grail, grailexp test files

[Doug Hyatt]

Jason Stajich wrote:

> Quick project for anyone wanting to jump in to bioperl, just speak up and
> you can have it be yours!
>
> I've added grail and grailexp output files to t/data/HUMBETGLOA.grailexp,
> t/data/HUMBETGLOA.grail .
>

Hello,

I suppose it makes sense for me to take this on, being the author
of GrailEXP and the one most familiar with the outputs.  Somewhat
complicated, as GrailEXP predicts genes, polyas, promoters, cpgs,
alternatively spliced genes that omit/insert exons, complete lists of ESTs
that hit each gene, and repetitive elements... so it probably has
to use a lot of different bioperl objects.

In addition, GrailEXP's alignment program can read Genscan
output files and do the EST search based on them, so there
should probably be some interaction with Bio::Tools::Genscan...

Also, should probably be set up like Blast, with the ability to
dispatch queries to the ORNL Grail server via Bioperl or to run
it standalone (grail/grailexp is available free to academics at
http://compbio.ornl.gov/grailexp/ ,
although it's no easy task to set up search databases for the program,
so most people just use our servers.)


>
> If anyone wants to write Bio::Tools::Grail which would be a gene
> prediction parser, and would have a method next_feature which would return
> Bio::Tools::Prediction::Gene objects.
>
> I've started and committed Bio::Tools::Grail so the gauntlet is thrown
> down if anyone wants to come in and finish it.  You get to add your name
> to the AUTHOR field too!  Very exciting I know. =)
>

=)

>
> -jason
>
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center
> http://www.chg.duke.edu/
>
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bye,
doug

Doug Hyatt
hyattpd@ornl.gov
Computational Biology
Oak Ridge National Laboratory
http://compbio.ornl.gov/