[Bioperl-l] annotation tools

[David Waring]

I know this is a little off topic but I hope someone in these groups can
help.

I will be starting to annotate human genomic sequences that we are finishing
here at the UWGC. I have been looking for tools to run genscan and then
blast predicted genes, and eventually (after some human intervention) get
these into a database (probably Ensembl).  It seems that both bioperl and
biojava have plenty of classes designed toward this purpose. Certainly these
tools exist but perhaps only in versions too customized for general usage.
Can anyone shed some light on the status of such tools?

Does anyone have a parser for genscan output (Perl or Java)?


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|   David Waring
|   Systems Programmer
|   University of Washington Genome Center
|   dwaring@u.washington.edu
|   (206) 221-6902
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