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:
ftp.infobiogen.fr:/pub/logiciels/mac/biology/clustalw.sea.hqx
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
