BepiPred 1.0		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   BepiPred predicts the location of linear B-cell epitopes in proteins using
   a combination of a hidden Markov  model and a propensity scale method. The
   method is described in detail in the following article:

   Improved method for predicting linear B-cell epitopes.
   Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen.
   Immunome Research 2:2, 2006.

   More information about the method can be found at:
   
      http://www.cbs.dtu.dk/services/BepiPred/


   DOWNLOAD

   The BepiPred 1.0 package  is a property of  Center for Biological Sequence
   Analysis.  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?bepipred

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


   PRE-INSTALLATION

   BepiPred 1.0  will run on the most common  UNIX platforms e.g. Linux.  The
   package consists of two files:
  
       bepipred-1.0.readme        this file
       bepipred-1.0.<unix>.tar.Z  compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install. After
   installation BepiPred will occupy at most 15 MB of diskspace.


   INSTALLATION

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

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

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

      cat bepipred-1.0.<unix>.tar.Z | uncompress | tar xvf -

      This will produce a directory 'bepipred-1.0'. The size of the installed
      package is at most 15 MB, depending on which binaries are included.

   2. Edit the paragraph labelled "GENERAL SETTINGS, CUSTOMIZE" at the top of
      the file "bepipred". Configure the following variables:

	    variable	    set to the full path to:
	    ---------------------------------------------------------
	    BP  	    'bepipred-1.0' directory
	    TMP 	    location for temporary data e.g. /var/tmp
	    ECHO	    'echo' executable
	    AWK 	    'awk' executable
	    PERL	    'perl' executable
	    --------------------------------------------------------

      Make sure that the settings you enter point at existing and operational
      utilities. You might need to modify them after the testing (see below).

   3. Make sure that the directory specified  by the variable TMP (see above)
      has the sticky bit set.  The listing should read  "drwxrwxrwt ...".  If
      the sticky bit is not set, set it:

      chmod 1777 <dir name>

   4. Test the package:
   
      ./bepipred test/CHO.fsa           # one sequence
      ./bepipred -t 0.90 test/CHO.fsa   # one sequence, higher threshold
      ./bepipred Pellequer.fsa          # many sequences

   5. Copy the 'bepipred' script to a directory in the users' path.

   6. Copy the 'bepipred.1' file to a appropriate location in your manual
      system. If you need a compiled version try running:

      man -d bepipred.1 | compress >bepipred.Z

      or:

      neqn bepipred.1 | tbl | nroff -man | col | compress >bepipred.Z

   7. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the BepiPred method  should be sent
   to Jens Erik Pontoppidan Larsen, jepl@cbs.dtu.dk

   CBS, 5 Mar 2007
   K. Rapacki