GFS: Genome-based peptide fingerprint
scanning. Use this software to match MS (and now MS/MS)
data to a genomic sequence. Available via our website or for download as open source. Presently the
download version is ready for Mac OS X only. However,
we have an internal version that runs on Debian Linux and is currently being
tested and packaged. Expect a Windows version to soon
follow. We would love to hear from you if you are
using GFS!
PROCLAME: The protein cleavage and
modification engine. This software is for predicting
possible combinations of post-translational modifications
on intact proteins, using an intact mass measurement and a
protein sequence from a database. It uses a search bounded
by fuzzy-logic based constraints. The website is here. We are readying a
standalone version, which is Java based.
Basefinder: Originally developed on the
NeXT platform starting 1991 and later brought to Mac OS X,
this software is used for signal processing and base
calling for DNA sequencing traces from either slab gels or
capillaries. Recently, we have been applying it to the
analysis of SHAPE data as well. A new download will
be available soon - check back here.
FreqAnal: Frameshift
prediction using heptamer statistics.
The program is on our download
page.
Its
original home is here.