[Bioperl-l] StandAloneBlast -> bl2seq case

Marcel van Batenburg marcelvb@nikhef.nl
Sat, 13 Oct 2001 21:13:47 +0200 (MET DST)

Dear group,

I downloaded the package bioperl (the version before the last
version), for I'm interested of using some bioperl modules. 
By the way I'm working on an operating system called Solaris. 
This system is used by more people, so I have not yet installed
the bioperl modules in general perl directories.

I'm employing your package to align one dna sequence of fixed length
with other sequence using blast. I used the executable bl2seq. How can
one run this executable in a loop (so more than once) without 
being stopped by EXCEPTION message, and how can one align a dnasequence
with less than 11 nucleotides without being confronted with the
same EXCEPTION message? 
The bl2seq could align a dnasequence with less than
11 consequtive nt when one makes a dna sequence of 11 nt by adding to its
flanks, IUPAC symbol N. The module IUPAC.pm could give me all possible 
sequences. Subsequently, one loops thru these sequences when aligning 
to a fixed second dnasequence. This will work if the excutable does not
terminate the holy workings of my perl script due to a detected 
misalignment (alignment is according to bl2seq an aligment of more than/or
equal to 11 consecutive basepairs).
Another solution is also welcome.

I'm looking forward to your reply,


P.S. Hopefully, I will never see any if-then-else-if statements. Gosh, A
     true object-oriented code should handle the choices of the user via
     its data structure.