[Bioperl-l] Finding mutations in Blast files

Gabriel Ab gabriel.jabud at gmail.com
Tue Jul 20 14:36:54 EDT 2010

I'm trying to write a script to find mutations in a Blast output file.  
The result should look something like [A/G] (query/subject) for SNPs and
[--/AT] for In/Dels.  I also need 50 bases both upstream and downstream if
I was able to get both the query and subject sequence extracted from blast
files, but parsing through that for mutations without the help of modules
and writing them like above is harder than it sounds.  Deletions and other
things in the alignment can make it very tricky.  I tried looking for
modules that would make this task easier but I couldn't find anything.  

Can someone point me in the right direction on how to do this or let me know
about modules that could help?

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