PROMOTER SCAN 1.7

[Ri-Ya Yang/SBR4/354.9980]

Where to find it?

On Fri, 26 Jan 1996 danp at biosci.cbs.umn.edu wrote:

> >>> 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.
> 
> 
>