DNA software

[Harry Mangalam]

Praveena V. Raman writes:

>Is there any software that
> can search a gene promoter for consensus
>binding sites
> of transcription factors?  Any help would be greatly
>appreciated.

   If you mean that you want to find a degenerate binding site in a
sequence, there are a number of programs that will do the trick, including
the "Findpatterns" program in the GCG package which uses a 'regular
expression' type of pattern matching.  If you mean that the software should
match a database of binding sites to the sequence of interest, you might
try try SignalScan by Dan Prestridge.  Part of the 'readme.doc' follows.

  Signal scan is a program developed to facilitate the analysis of DNA 
sequences for known eukaryotic signals.  This program is FREE. You may copy 
and distribute this program, but you may not charge for its distribution. 
You MUST register the program by sending your name and address to the below 
address. Registering this program helps to justify the program for funding 
purposes.  For registering the program you will automatically be notified of 
SIGNAL SCAN changes and updates. PLEASE REGISTER, you will help assure the 
future development of SIGNAL SCAN.  Note that if you have ordered the 
program directly from me, you are already registered.
  The source code is written in the `C' language and is fairly easy to port
over to other hardware and operating systems.  The source code will be made
available upon request. You may make changes to the source code, but may not 
release the modified program or source code without my authorization.
  If you use this program in published research, please cite:

Prestridge, D.S. (1991) SIGNAL SCAN: A computer program that scans DNA 
sequences for eukaryotic transcriptional elements. CABIOS 7, 203-206.

  The author welcomes comments and suggestions on the program or additions
to the database.  Please contact and send registration to:

  Dr. Dan S. Prestridge                        tele:(303) 465-0658
  Dept. of Mol., Cell., and Devl. Biology      email:DANP at BEAGLE.COLORADO.EDU
  University of Colorado
  Boulder, Colorado   80309-0347



   There's also an older Mac version still available (I think) on
ftp.bio.indiana.edu (or from me - I just found it buried in a very deep
folder).

   The unix version is really quite useful and easy to set, update, and use.
Cheers
Harry