Bioperl: BioPerl module for HSPs..

[Geetha Vasudevan]

Wondering if there is a module that can extract HSP alignments for the
query set from the BLAST_OP.  The SEALS module BLAST2BOUNDED does that
but if the query set is a
nucleotide, it is not possible.
This SEALS module reads the HSP bounds from the BLAST_OP but
performs a "gi2fasta" to retrieve the sequences from Entrez. If it is
nucleotide, one would want the translated sequences available in the
BLAST_OP.

Any help would be highly appreciated.
Thank You.

--
Geetha Vasudevan
W. M. Keck Center for Informatics
Institute of Biosciences and Technology
The Texas A&M University System Health Science Center
2121 Holcombe, Houston, TX 77030
Fax: 713.677.7414
Tel: 713.677.7704
email: geetha@blackbolt.ibt.tamus.edu
http://xian.tamu.edu/



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