Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!usc!nic.csu.net!beach.csulb.edu!csus.edu!wuarchive!zazen!psl.wisc.edu!psl.wisc.edu!LONETTO
From: lonetto@psl.wisc.edu
Newsgroups: bionet.software
Subject: <None>
Message-ID: <1991Apr30.034557.5624@pslu1.psl.wisc.edu>
Date: 30 Apr 91 03:45:57 GMT
Sender: news@pslu1.psl.wisc.edu (USENET News System)
Reply-To: lonetto@psl.wisc.edu
Organization: University of Wisconsin - Physical Science Lab
Lines: 24

I'm writing to ask for help.  I've been doing a sequence analysis project on a
group of related proteins.  I have a set of 23 related sequences that I've been
able to align and now I want to do some analysis on the potential protein
structures involved.  Does anyone out there have any code (preferably Pascal or
C) that will generate the "raw" data for structure prediction according to
Garnier et al. (JMB.120:97-120(1978))??  I need to get the numbers directly (NOT
the predictions) since I want to expand the analysis by taking the sequence
alignment into account.  Basically, I want to average the values by position and
then subtract a penalty from the helix and beta-sheet scores for gaps in other
sequences at the position.  I have a paper where a similar procedure was used
(Zvelebil et al. JMB.195:957-961(1987)).  I have programs here that generate the
predictions, but as you can see, that doesn't do what I need.  I have access to
unix, VMS and Macintosh in easy reach.  If I have to I can borrow a DOS
machine.  At present the "common" format my alignments are in is
intelligenetics, with .'s for gaps.

For that matter, does anyone have versions of standard programs (hydropathy,
hydrophobic moment, composition bias) adapted for use on multiple sequence
alignments?

Thanks,

Mike Lonetto   lonetto@psl.wisc.edu   (608)262-4620 / 262-4828