TargetP 1.1		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   TargetP predicts the subcellular location of eukaryotic protein sequences.
   The assignment is based on the predicted presence of any of the N-terminal
   presequences:  chloroplast transit peptide (cTP),  mitochondrial targeting
   peptide (mTP)  and  secretory pathway signal peptide (SP).  The method  is
   described in detail  in the following article:

   Predicting subcellular localization of proteins based on their N-terminal
   amino acid sequence.
   Olof Emanuelsson, Henrik Nielsen, Soren Brunak and Gunnar von Heijne.
   J. Mol. Biol. 300:1005-1016, 2000.

   More information about the method can be found at:

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

   DOWNLOAD

   The TargetP 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?targetp

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


   PRE-INSTALLATION

   TargetP 1.1 will run on the most common  UNIX platforms e.g.  Linux, SunOS
   etc. The package consists of two files:
  
       targetp-1.1.readme	 this file
       targetp-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)
	perl	(        /usr/bin/perl)
	nawk	(or equivalent, e.g. gawk)
	sh	(usually /bin/sh)
	echo	(        /bin/echo)


   INSTALLATION

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

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

      This will produce a directory 'TargetP-1.1'.  The size of the installed
      package is at most 7 Mb, depending on which binaries are included.

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

		Variable	Set to the full path to:
		-------------------------------------------
		TARGETP		'targetp-1.1' directory
		TMP		location for temporary data
		PASTE		'paste' executable
		PERL		'perl' executable
		AWK		'awk' executable
		SH		POSIX-compliant shell
		ECHO		'echo' 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. Edit the paragraph  labelled  "HELPER APPLICATIONS, CUSTOMIZE"  further
      down in the same file. Configure the following variables:

		Variable	Set to the full path to:
		----------------------------------------
		CHLOROP		'chlorop' executable
		SIGNALP		'signalp' executable

      TargetP will need those softwares to produce the output as described in
      the reference quoted above. They will be employed if the '-c' option is
      used but not otherwise.  The decision whether to install them should be
      with the future users of TargetP:
      
      * if prediction of chloroplast transit peptide cleavage sites is needed
        you will have to install ChloroP;

      * if prediction of secretory pathway  signal peptide  cleavage sites is
        needed you will have to install SignalP.

      ChloroP and SignalP can be obtained by mailing software@cbs.dtu.dk.

   4. 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>

   5. Test the package:
   
      ./targetp -P test/one.fsa			# one sequence
      ./targetp -P test/twelve.fsa		# many sequences

      If all the output values are equal to 0 (zero)  increase the swap space
      on the machine.

   6. Copy the 'targetp' script to a directory in the users' path.

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

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

      or:

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

   8. Enjoy ...


   PROBLEMS

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


   CBS, 6 Feb 2007
   K. Rapacki