[Biopython-dev] Bio.CAPS module submission

[Jonathan Taylor]

I have been doing a fair amount of work using CAPS markers for 
genotyping.  A CAPS marker is essentially a pair (snp, enzyme) where the 
snp is the location in a set of sequences (an alignment) in which a 
polymorphism causes an enzyme to cut differentially.

I'm interested in contributing a module that does most of the work for 
me.  I am willing to maintain it and provide documentation.  It already 
has a few unittest test cases.

The module's main function is in the CAPS.CAPSMap class.  This class 
takes a Bio.Align.Alignment object and uses the Bio.Restriction package 
to find all the (possible) CAPS markers within the alignment and to 
provide information to build caps marker based programs.

The module is at:
http://bbc.botany.utoronto.ca/~jtaylor/CAPS/

Regards,
Jonathan Taylor.
University of Toronto Botany Department.