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 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