stand-alone equivalent of PRETTY

Scott Givan givan at molbio.uoregon.edu
Fri Nov 1 03:41:36 EST 1996

In article <55b1ju$joc at netnews.upenn.edu>, lklimcza at mail1.sas.upenn.edu
(Les Klimczak) wrote:

>         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.
>         Does anyone know of any stand-alone program/macro/script that 
> would perform this function? TIA.
>         Les Klimczak
> _____________________________________________________________________
> Dr. Les J. Klimczak           |  mailto:lklimcza at sas.upenn.edu
> Department of Biology         |  http://www.sas.upenn.edu/~lklimcza
> University of Pennsylvania    |  Tel.:     (215) 898 3673
> Philadelphia, PA 19104-6018   |  FAX:      (215) 898 8780
> _____________________________________________________________________

I've had good luck using a program called "clustalW" on my mac.  I believe
it uses a similar algorithm to PRETTY to find amino acid similarities
between proteins.  It also has the capability of formatting its output in
several file formats.  I believe the version I use currently is 1.6. 
clustalW on my mac is usually quite a bit slower than PRETTY (running on
sgi platform), but it fits the bill sometimes.  In a cursory search, it
looks like you could FTP clustalW from the following site:


This is of course a mac version, but I think it comes in all the popular
flavors.  I hope this helps.

Scott Givan
University of Oregon
Institute of Molecular Biology
givan at molbio.uoregon.edu

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net