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From: roy@phri.UUCP (Roy Smith)
Newsgroups: net.wanted,net.bio
Subject: Wanted: sequence analysis software for Unix (and a proposal)
Message-ID: <184@phri.UUCP>
Date: Fri, 15-Feb-85 14:47:12 EST
Article-I.D.: phri.184
Posted: Fri Feb 15 14:47:12 1985
Date-Received: Sun, 17-Feb-85 06:34:18 EST
Distribution: net
Organization: Public Health Research Inst. (NY, NY)
Lines: 39
Xref: watmath net.wanted:5808 net.bio:170


	I am looking for genetic (DNA and Protein) sequence analysis
software which runs under Unix.  In particular, I am right now on the
hunt for a program which does protein secondary structure prediction
(Chou-Fasman or other algorithms).

	 I hope the scientists out there don't take this as an insult
(it's not meant as one), [flame on] BUT I AM SICK OF TAKING PROGRAMS
WRITTEN IN DISGUSTING VMS FORTRAN, LOADED WITH COMPUTED GOTOS AND MAGIC
NUMBERS, MISSING ANY REASONABLE DOCUMENTATION OR COMMENTS, AND
CONTAINING INSEPERABLY IMBEDDED CODE TO ACT AS A SCREEN MANAGER AND
PLOTTER DRIVER FOR SPECIFIC DEVICES AND BEATING THEM INTO SHAPE TO RUN
UNDER UNIX [flame off].  Does there exist a list of sequence analysis
programs which run under Unix and are available for public consumption?

	On the assumption that no such list exists, how do we go about
starting one up?  How about this: if you have sequence analysis software
which runs on Unix and are willing to give it away, send me a list of
what you have and I will make a summary of it to net.bio.

	I have written a set of programs to do the usual restriction
mapping, homology searches, generation of reverse complements, etc., all
with standard Unix-style syntax (i.e. command line arguments, usable as
filters, free-format input).  Before I go too far, I want to know what
work (if any) has been done on setting standards for sequence analysis
software (for Unix in particular, or otherwise).  If nothing already
exists, then can we (i.e. the professional programmers who write
sequencing software) get together and work some out?

	Send program lists directly to me; other responses post to
net.bio; perhaps we can get a discussion going on this issue.
-- 

The opinions expressed herein do not necessarily reflect
the views of the Public Health Research Institute.

{decvax,ihnp4}!vax135!timeinc\
                              >!phri!roy (Roy Smith)
     {allegra,rocky2}!cubsvax/