[Bioperl-l] genbank (blast) alignments

Thomas Keller kellert at ohsu.edu
Wed Jul 22 13:17:03 EDT 2009

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?


kellert at ohsu.edu

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