[Bioperl-l] using bioperl to compare sequences

[Ben Bimber]

Hello,

I have a couple years programming experience, but am reasonably new to
perl and extremely new to bioperl.  I have been reading through the
bioperl documentation and am trying to understand the best way to
approach a particular problem.  I'm hoping someone could offer some
tips and point me in the right direction.  If someone has solved this
sort of problem before, i'd prefer not to reinvent things.  Here's
what I'm trying to do:

Our lab generates mRNA sequence data, consisting of alleles of a given
gene or genes
I want to compare each of these sequences against a reference using
BLAST or clustalw (will need the ability to choose at run time)
Take the result of this alignment, then record positions of difference
between the experimental sequence and reference sequence (SNPs)
Translate the corresponding AA change(s) associated with each SNP.
There can be overlapping ORFs.

I see that bioperl has modules for BLAST and clustal.  I've also been
looking at the modules under variation.  I havent fully wrapped my
head around them, but they look to be what i'd use for SNP detection.

has anyone has written code to perform similar things and if so, would
you be willing to share specific examples?  Anything concrete to see
exactly how these modules operate would be extremely helpful.

Thanks in advance for any tips or help.