[Bioperl-l] genbank (blast) alignments

[Thomas Keller]

Greetings,
Blast 2.2.21 has a multi-sequence alignment feature that is really  
handy: put in the accession number of the refseq in one sequence field  
and a concatenated fasta file of the Sanger reads to align in the  
second box and it does the alignments. Unfortunately, the output is a  
series of alignments rather than the more useful msf format with all  
reads aligned with the reference.

Is there a bioperl module that reads the blast alignments and converts  
it to an msf alignment?

thanks,


Tom
kellert at ohsu.edu
503-494-2442