[Bioperl-l] mis-match position in HSP

[Sucheta Tripathy]

Hi,

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


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606