PROMOTER SCAN 1.7

Dan S. Prestridge, Ph.D. danp at biosci.cbs.umn.edu
Fri Jan 26 10:35:29 EST 1996


>>> ANNOUNCING THE AVAILABILITY OF PROMOTER SCAN version 1.70 for UNIX & IBM PC:

NOTE THAT THIS IS A CORRECTIVE UPDATE. Previous versions of PROMOTER
SCAN did not analyze the opposite strand correctly (see below). This
has been corrected, and you should upgrade any previous version of
PROMOTER SCAN with this version.  Below are the changes made in
version 1.70.

NOTE THAT THE NEW IBM PC VERSION WILL RUN ONLY IN A WINDOWS 95 DOS
WINDOW (See details below)!

REGISTRATION NOTE: please register with every new version of PROMOTER
SCAN that you install. Due to the changing nature of Email addresses
and personal interests, only users registered for the past or current
version are notified of corrections and updates. To register, please
send a brief message, such as "register promoter scan", to
danp at biosci.cbs.umn.edu. If you obtain information on how to get the
program from direct inquiry to me, you are automatically registered.
While this will take very little effort on your part, it makes my life
a lot easier. Thanks.

1/96
VERSION 1.70

PC VERSION NOTE:
Note that PROMOTER SCAN version 1.7 MUST be run under WINDOWS 95!
It will run in a DOS window in Win95, and must be run in the 32-bit
DOS that is only in Win95 (it may also run in Win NT, or if you are
running 4DOS or other 32-bit DOS system -- I have not tested these
configurations).  Sorry for any trouble, but there are several
reasons that this has been done.  Since my time is VERY limited, and
I want to spend most of it doing research, and the NIH is not 
interested in funding this project, I must limit the number of 
operating systems (to UNIX and Win95), make the source code as
EASY as possible to port between them, design the source code
such that as few changes as possible need to be made to change it
from experimental to distribution code, and allow the PC to analyze
the same sequence lengths as the UNIX version does.  Also, in keeping
with a simpler model for the source code, the fancy PC text graphics
have been eliminated, and you must now press the return key after
every menu selection. The UNIX and PC versions of the program are 
now almost identical. One of these days, if I ever have any funding,
I would like to make a Windows95 Graphical User Interface, with
graphs of promoter predictions.  But considering the present funding
situation, don't look for it anytime soon.

1) In previous versions of PROMOTER SCAN, the opposite strand was not
   analyzed symmetrically to the top strand. As a result, if you
reverse-complemented a DNA strand, and analyzed it, promoter locations
were not symmetrical with the opposite analysis.  Corrections have now
been made so that the analysis is symmetrical. The resulting data from
tests have shown that this increased the number of false-positive
predictions, such that the false-positive rate has increased to about
one in 14,000 bases while recognizing approximately 70% of primate
promoter sequences. The effect of this on your predictions is
uncertain, however, you should ru-run any sequences of interest if
there is a possibility that there may be promoter sequences on the
opposite strand.

2) You may run PROMOTER SCAN from the command line by using the
"prorun" command. You may have to change this script to fit your
operating system, it is written for Sun Solaris, but should work on
most UNIX systems. Run the command as "prorun seqname.seq"
substituting "seqname.seq" with your sequence name. You can easily
modify this script to run a list of sequences.

3) PROMOTER SCAN now takes sequences up to 500kb.

4) Most source statements causing ANSI C compiler warnings on some
machines should now be corrected.

5) TFD site reference numbers are output into the results. You can
reference these sites using SIGNAL SCAN. 

6) Note that the UNIX version works best in an XTERM or from a VT
terminal window.  It does not work well in a Sun command tool window.

7) The source should compile now on some platforms that are affected
by return escape codes at the end of lines, these have been removed.

8) Some test screen graphics problems have been resolved and improved.

9) Results are now recorded in a file named "prediction".

10) Handling of GCG formated sequences has been made more robust.





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