[Bioperl-l] IUPAC support for DNA alignment

Yee Man Chan ymc at shgc.stanford.edu
Thu Jun 26 14:13:04 EDT 2008


Hi all

	I am the owner of Bio::Tools::dpAlign. A user emailed me to add
support for IUPAC nucleotide codes. I am ok to add this feature but I
would like to know what are the conventions to handle these IUPAC codes.

	Suppose match is +3 and mismatch is -1. Then what should be the
score when T matches with U, A with W, A with D, A with N and A with X?
Does anyone know the conventions?

Thanks a lot.
Yee Man


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