charles at MEDINFO.ROCHESTER.EDU ("Charles A. Alexander") writes:
>Here's an interesting problem. ... (much deleted) ... looking only for
> homology (not >"Dis-Homology").
I'm posting in case I'm wrong and someone can shoot me down, but it seems
that for "dis-homology" you could use an inverse comparison table; e.g.,
a table where 'A' vs. 'A' is worth '0.0' while an 'A' vs. 'C' (or vs. 'G'
or 'T') is worth 1.0 -- this is opposite of the normal NWSGapDNA.Cmp table.
Using the inverse table, PileUp will look for the worst alignment instead
of the best.
-- Rick
Rick Westerman System Manager of the AIDS Center Laboratory
westerm at aclcb.purdue.edu for Computational Biochemistry (ACLCB), BCHM
Phone: (317) 494-0505 bldg., Purdue University, W. Lafayette, IN 47907
FAX: (317) 494-7897
