[Bioperl-l] mis-match position in HSP

Sucheta Tripathy sutripa at vbi.vt.edu
Tue Nov 2 20:35:24 EST 2004


Just a quick question, is there a method to get the mis match position
from a blast output using Bio::Search::HSP::HSPI.

For example if I have an HSP like this:

 5 atgaataggatagggataggtagata 26
   ||| ||||||||||||||||||||||
23 atgtataggatagggataggtagata 44

Then the mismatch position is 4.

Thanks in advance


Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
Fax:  (540) 231-2606

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