[Bioperl-l] Bio::Search::GenericHSP from cigar_line to pairwise alignment

Albert Vilella avilella at gmail.com
Mon Dec 15 06:31:58 EST 2008


Does anybody have a working tested way to go from a cigar_line back to
the pairwise alignment
coming from a GenericHSP (like blastp, etc)?

I can see that GenericHSP has the code for calculating the cigar_line
from the alignment,
but we (Ensembl) only store the cigar_lines, and would like people to
be able to go back
to the alignment in Bioperl. Just asking if anyone has done this
before I get my hands
dirty on it...



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