Restriction fragment mapping programs

Harry Mangalam mangalam at uci.edu
Sun Feb 14 19:25:14 EST 1999


There are 3 such apps that I remember offhand, all old. (Sorry if this
is a repetition - I didn;t see any previous postings.)
the first is one is COMAP for DOS, by Kay Hoffman - it will probably be
in the iubio archives.  It doesn't doe everything you want but it may
help. Here's the readme:
ftp://ftp.bio.indiana.edu/molbio/ibmpc/comap.readme

The second is part of Bill Pearson's old work, is a Fortran app and is
still available I think - hah! here it is (unix of course - don't know
if f2c will do it):
ftp://ftp.virginia.edu/pub/fasta/rest-map.shar

The third is a Mac / Sun app called...brain churning ... ahah Double
Digester, which is a lisp(?) app, but compiled in some way (I think) at: 
ftp://ftp.bio.indiana.edu/molbio/restrict-enz/double-digester/

Don't know if this is any help to you, but I've written an app that
while it doesn;t do what you want, might help in the analysis and
verification of what you want to do:
tacg will consume any amount of (possibly degenerate) sequence and spit
back restriction maps, fragment tables, gel simulations, translations,
ORFs, etc.

The currently released version can be got at:
ftp://mamba.bio.uci.edu/pub/tacg
and there's a webified version at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.form.html

That version is soon (within a month or so, hopefully) to be replaced
with version 3 BETA which adds matrix matching using the TRANSFAC
format, full regular expression matching, automagic sequence conversion
on input, support for analyzing multiple sequences at a time, searching
for silent sites, reverse translation, and a bunch of other stuff.  This
is on top of its previous ability to do restriction enzyme analysis of
unlimited sequence input (exact or degenerate), more general searching
for unlimited numbers of patterns (with errors), proximity matching, any
frame translation, yadda, yadda yadda.

It will be released in rpm format for RedHat linux, as well as
(hopefully) .deb format for Debian, as well as the usual tarball for
other unices (runs on all linuxes, IRIX, Solaris, Compaq Tru64 (aka
TUFKADUx (The Unix Formerly Known As Digital Unix), SPP-UX/HP-UX, and
others).
This will unfortunately be only the command-line version as I'm
completely re-doing the Web interface.

Cheers
Harry



apogee1 at my-dejanews.com wrote:
> 
> Hi!
> 
> Actually, I am in the same situation as Caro, and so I was glad to see her
> post. I would like to map an ~100kb insert and localize a 5kb stretch of
> known sequence in it. Looking at your program, I was quite impressed what it
> can do, but I couldn't see how it could help me in solving my problem, as it
> still seems to me that you have to enter the sequence data in order to get a
> map, and what I am looking for is a program in which I can enter used enzymes
> and fragment lengths obtained and assemble this data into a restriction map.
> Is there a way this problem can be solved with CloneIt? Or is there any other
> program around that can do it, either PC/Mac/Unix ?
> 
> Michael
> 
> In article <79bm8r$b26$1 at saphir.jouy.inra.fr>,
>   lindenb at jouy.inra.fr (Pierre Lindenbaum) wrote:
> > :I'm trying to find
> > : a program which will allow me input data from restriction digests,
> > : subsequently blotted and probed with known markers, and create a map of
> > : the digest pattern.
> > On the WWW you could try CloneIt
> > Hope it helps.
> 
> -----------== Posted via Deja News, The Discussion Network ==----------
> http://www.dejanews.com/       Search, Read, Discuss, or Start Your Own

-- 
Cheers,
Harry

Harry J Mangalam, Biological Chemistry
Rm 158, MedSciC, College Of Medicine, UC Irvine, Irvine, CA, 92697
(949) 824 4824[vox], (949) 824 2688[fax], 
mangalam at uci.edu || mangalam at home.com 
http://hornet.bio.uci.edu/~hjm/




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