> We are trying to become less dependent on the GCG package,
> especially since many PC- and Web-based programs provide parts of its
> functionality and the fees/costs of maintaining GCG have not declined in
> a noticable way. Our only "missing link" in making graphically enhanced
> sequence alignments in the function of PRETTY - identification of similar
> amino acids, as defined by a similarity matrix such as PAM250, and
> labeling of the identified ones with uppercase.
Pretty per se doesn't do any alignments; nor do the related programs
PrettyBox and PrettyPlot. The PileUp program does the actual
There are a couple of multiple sequence alignment programs out there.
Clustal is probably the oldest publically available program.
To replace PrettyBox itself I suggest looking at the BoxShade program by
Kay Hoffmann. I'm not sure if there is a PC-based replacement for
PrettyPlot although I suspect there should be.
Rick Westerman System Manager of the Ag Campus Lab. for
westerm at purdue.edu Computational Biology (ACLCB) & Sys. Mgr.
Phone: (317) 494-0505 of the Biochemistry department BCHM bldg.
FAX: (317) 494-7897 Purdue Univ. W. Lafayette, IN 47907