Bioperl: BioPerl module for HSPs..

Geetha Vasudevan
Mon, 07 Feb 2000 11:55:34 -0600

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

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

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