[Bioperl-l] parsing psiblast + ?

sisterdot therealsisterdot at gmail.com
Mon Mar 11 10:31:42 UTC 2013


hey hey, 

i am using perl v5.10.0 and Bio::SearchIO 1.006901

i would like to use psiblast 2.2.27 + (instead of blastpgp), but parsing 
via  
new Bio::SearchIO(-format => "blast",-file => "$file")
doesn't seem to work well- individual iterations are interpreted as 
separate results.

Bio::SearchIO doesn't seem to really understand "psiblast +" default 
pairwise output, or am i mistaken?
if i am not mistaken, are there alternatives in Bioperl for parsing 
"psiblast +" with the default "-outfmt 0"?

thanks a lot
sis



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