HMMgene 1.1		INSTALLATION INSTRUCTIONS


DESCRIPTION

HMMgene 1.1 is a program for prediction of genes in anonymous DNA. The program
predicts whole genes,  so the predicted exons always splice correctly.  It can
predict  several whole or partial genes in one sequence,  so it can be used on
whole cosmids  or  even longer sequences.  HMMgene can also be used to predict
splice sites and start/stop codons.  If some features of a sequence are known,
such as hits to ESTs, proteins or repeat elements, these regions can be locked
as coding or non-coding and then the program will find the best gene structure
under these constraints.  The method  is described in detail  in the following
article:

Two methods for improving performance of an HMM and their application
for gene finding.
A. Krogh.
Proc. of ISMB5, pages 179-186, AAAI Press, 1997.

More information about the method can be found at:

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

NOTE: all text above this line is by K. Rapacki, needed to generate the CBS
Software brochure.

HMMgene 1.1

Copyright (C) 1998 by Anders Krogh
All rights reserved.

The HMMgene package is obtained from
	Anders Krogh, krogh@cbs.dtu.dk

      ******   PLEASE DO NOT REDISTRIBUTE THE PACKAGE  ******


This software is provided ``AS IS'' and any express or implied
warranties, including, but not limited to, the implied warranties of
merchantability and fitness for a particular purpose, are disclaimed.
In no event shall the author be liable for any direct, indirect,
incidental, special, exemplary, or consequential damages (including,
but not limited to, procurement of substitute goods or services; loss
of use, data, or profits; or business interruption) however caused and
on any theory of liability, whether in contract, strict liability, or
tort (including negligence or otherwise) arising in any way out of the
use of this software, even if advised of the possibility of such
damage.


INSTALLATION:
=============

The package is packed with tar and possibly compressed (gzip) and
uuencoded.

It unpacks in a directory called hmmgene1.1

The directory contains these files:

	README		This file
	hmmgene		A perl script which is used to run the gene finder.
			You need perl 5.
	HMMgene		The program that does the main job
	hmmgene1_1.ps	User's guide. Postscript.
	lib/		Directory containing several files necessary for
			the program to run.

After unpacking the directory you should

1.  Move the directory lib to whereever you want it (if not where it
	already is).
2.  Move the executables hmmgene and HMMgene to /usr/local/bin or
	any other place you like.
3.  In the perl script hmmgene, change the directory names
	$bindir and $libdir.
4.  Print hmmgene1_1.ps and read it.
5.  Run the program.