ChloroP 1.1		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   ChloroP predicts  (i) the prescence of chloroplast transit peptides (cTPs)
   in protein sequences and  (ii)  the location of  a potential  cTP cleavage
   site in each input sequence. The method is described in detail in the
   following article:

   ChloroP,  a neural network-based method for predicting chloroplast transit
   peptides and their cleavage sites.
   Olof Emanuelsson, Henrik Nielsen and Gunnar von Heijne.
   Protein Science 8:978-984, 1999.

   More information about the method can be found at:

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


   DOWNLOAD

   The ChloroP 1.1 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?chlorop

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


   PRE-INSTALLATION

   TargetP 3.0 will run on the most common  UNIX platforms e.g.  Linux, SunOS
   etc. The package consists of two files:
  
        chlorop-1.1.readme	 this file
        chlorop-1.1.<unix>tar.Z	 compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install.  Make
   sure that the following programs are available on your system:

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


   INSTALLATION

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

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

      cat chlorop-1.1.tar.Z | uncompress | tar xvf -

      This will produce a directory 'chlorop-1.1'. The size of the
      uncompressed package is at most 3.5 Mb, depending on which binaries
      are included.

   2. Edit the paragraph labeled "GENERAL SETTINGS, CUSTOMIZE" at the top
      of the file "chlorop":

      CHLOROP	full path to the 'chlorop-1.1' directory (mandatory)

      PASTE	      "		 'paste' executable
      AWK	      "		 'awk' executable (or gawk, nawk etc.)
      SH	      "		 POSIX-compliant shell

      You might need to alter the settings after the testing.

   3. Make sure that the 'tmp' directory has the sticky bit set. The listing
      should read "drwxrwxrwt ...". If the sticky bit is not set, set it:

      chmod 1777 tmp

   4. Test the package:
   
      ./chlorop test/test1.fsa			# one sequence
      ./chlorop -F test/test1.fsa		# one sequence, full output
      ./chlorop test/test12.fsa			# many sequences
      ./chlorop -F test/test12.fsa		# many sequences, full output

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

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

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

      or:

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

   7. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects  of the ChloroP method  should be sent
   to Olof Emanuelsson, olof@sbc.su.se.

   CBS, 7 Feb 2007
   K. Rapacki