[Bioperl-l] Calculating a bunch of SNPs

Amir Karger akarger at CGR.Harvard.edu
Thu Jan 19 12:15:41 EST 2006


I have 96 files. The first is a reference sequence. The other 95 are
sequences from different genotypes, with minor SNPs compared to the first
one. I want to generate a list of all the SNPs for each sequence compared to
the reference sequence. Output format doesn't really matter.

I was told I could run EMBOSS diffseq on each of the 95 pairs, and parse the
output to get my list. I'm wondering if there's a Bioperl tool that will do
what diffseq does, though - presumably outputting Bio::Align objects of some
kind, or is it Bio::Variation? - rather than parsing 95*N output files.

Thanks,

- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
Harvard University
617-496-0626


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