[Bioperl-l] matrix from bl2seq

[kevin.mcmahon at ttuhsc.edu]

Giovanni,
 
I am new to Bioperl myself, so take my advice with a grain of salt.  But, it
sounds like you've got the right idea.  If you're looking to make one of
those charts that shows the percent identity between two sequences for every
permutation, I'd do exactly what you're doing.  And use the frac_identical
or frac_conserved (depending on what you want) methods from the
Bio::Search::Hit module.  For real information on how to do this, check out
Jason Stajich's excellent review on the Bio::SearchIO module here:
http://bioperl.org/HOWTOs/html/SearchIO.html
<http://bioperl.org/HOWTOs/html/SearchIO.html> .  It sure helped me!
 
Good luck,
 
Wyatt