Promoter 2.0		INSTALLATION INSTRUCTIONS


DESCRIPTION

Promoter is a program for predicting vertebrate PolII promoters in DNA
sequences. The method is described in detail in the following article:

	Promoter 2.0: for the recognition of PolII promoter sequences.
	S. Knudsen.
	Bioinformatics, 15:356-361, 1999.

More information on the method is also available at:

        http://www.cbs.dtu.dk/services/Promoter/

For a favorable comparison of this software to other promoter prediction
software, see:

	J.W. Fickett and A.G. Hatzigeorgiou
	Eukaryotic promoter recognition.
	Genome Res., 7(9): 861-878, 1997


DOWNLOAD

Promoter 2.0 is Copyrighted 1994-1998 by Steen Knudsen and all rights are
reserved. It may be downloaded  only  by special agreement. For academic
users  there is a download site at:

     http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?promoter

Other users are requested to contact software@cbs.dtu.dk.


PRE-INSTALLATION

Promoter 2.0  will run on the most common UNIX platforms e.g. Linux,
SunOS etc. The package consists of two files:

     promoter-2.0.readme		this file
     promoter-2.0.<unix>.tar.Z		compressed TAR archive

where 'unix' is the UNIX platform on which you are about to install.


INSTALLATION

0. Make sure that the following programs are available on your system:

	uname	(usually /bin/uname)
	echo	(        /bin/echo)
	nawk	(or equivalent, e.g. gawk)

1. Decide where you wish to keep the software. Uncompress and untar
   the package in that location:

	cat promoter-2.0.tar.Z | uncompress | tar xvf -

   This will produce a directory 'promoter-2.0'. The size of the
   uncompressed package is at most 5 Mb, depending on which binaries
   are included.

2. Edit the paragraph labeled "GENERAL SETTINGS, CUSTOMIZE" at the top
   of the file "promoter". It is essential that the variable 'PROM' be
   set to the full path to the 'promoter-2.0' directory.

   You might need to alter some settings after the testing.

3. Test PROMOTER on the test sequence shipped with the package:

	cd $PROM
	./promoter test/test.seq

   The output should be identical to the file 'test/test.seq.out'.
   You might like to perform other tests:

	./promoter -f test/test.seq	# full output
	./promoter -w test/test.seq	# HTML

4. Copy the 'promoter' script to a directory in the users' path.

5. Copy the file 'man/promoter.1' to an appropriate location in your manual
   system. If you need a processed version use 'man/promoter.Z' instead.

6. Enjoy ...


PROBLEMS

Contact packages@cbs.dtu.dk in case of problems.

Questions on the scientific aspects of the Promoter method  should be sent
to Carsten Friis, carsten@cbs.dtu.dk.

CBS, 20 Jun 2007
K. Rapacki