roy@phri.UUCP (Roy Smith) (02/15/85)
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/roy@phri.UUCP (Roy Smith) (02/17/85)
> I am looking for genetic (DNA and Protein) sequence analysis > software which runs under Unix. [...] > 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 [...] From the response I got to my earlier posting, it is clear that my meaning has been mis-understood. My intention was NOT to ridicule scientists who write and distribute software. Rather, it was to point out that it would be to the advantage of everybody involved if those people with formal training in programming who write software for the biological sciences were to get together and 1) let people know what is already available and 2) get together and write some standards which would make our lives a bit easier. -- 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/
schuster@Shasta.ARPA (02/19/85)
-=-
When I was an undergrad at Cornell, I worked writing a bunch of sequence
analysis programs in Pascal which I subsequently optimized into assembler
to run on an Apple II. But the Pascal was relatively portable, and
I believe that you can get a hold of the programs and source by
writing to (Yes, that's snail mail) to
Dr. John Lis
Dept. of Biochemistry
Wing Hall
Cornell University
Ithaca, NY 14853
Of course, you wanted UNIX and not Apple II, but it might be a start
for people who do use micros in their labs. They do simple sequence
analysis of proteins and NA sequences. They can also plot homologies
on a graph. The programs worked for sequences up to about 32K bases
long. He can probably also put you in touch with someone who has a
program that allows you to use a digitizer to input the bands from a
restriction digest and calculates the order of the fragments.
I hope that this, though not exactly what you asked for, is
of help to someone.
Ah, Biochemistry, my true love, but I was a klutz, hated labwork, and
had been working on computers for too long to give them up.
Jay Schuster,
schuster@{su-shasta,su-gregorio}.arpa
...!decwrl!glacier!shasta!schuster