In identifying peptides from proteins with a known sequence, it is often useful to be able to predict how a peptide will migrate during electrophoresis, chromatography, or two-dimensional peptide mapping.
The Pepsort program, which runs as an add-on to the GCG/UW package of sequence analysis programs, will calculate electrophoretic and chromatographic mobilities for peptides derived from a sequence file. This is a program written by at the Salk Institute by Lisa Caballero using data of Tony Hunter's. It is by no means foolproof, but can predict the mobilities of some peptides very accurately.
To run Pepsort, you need to have the GCG sequence analysis package on your computer.
You can obtain Pepsort from the Salk Institute by ftp with your browser using this link
This directory contains a readme file that explains what to download and how to run the program.
Parts of the readme can be found on this linked page.
Pepsort is used in conjunction with a program called Mobility that will plot the predicted mobilities of your peptides. It is included in the same ftp directory on axp1.salk.edu.