NetOGlyc 3.1		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   NetOGlyc predicts  mucin type O-glycosylation sites  in mammalian proteins
   using  a cluster of neural networks.  The method is described in detail in
   the following article:

   Prediction, conservation analysis and structural characterization of
   mammalian  mucin-type  O-glycosylation sites.
   K. Julenius,  A. Mølgaard, R. Gupta and S. Brunak.
   Glycobiology, 15:153-164, 2005.

   The earlier versions of NetOGlyc are described in:

   NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence
   context and surface accessibility.
   J E Hansen,  O Lund, N Tolstrup, A A Gooley, K L Williams and S Brunak.
   Glycoconjugate Journal, 15:115-130, 1998.

   Prediction of O-glycosylation of mammalian proteins: Specificity patterns
   of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase.
   J E Hansen, O Lund, J Engelbrecht, H Bohr, J O Nielsen, J E S Hansen and
   S Brunak.
   The Biochemical Journal, 308:801-813, 1995.

   Related paper:

   O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
   R Gupta, H Birch, K Rapacki, S Brunak and J E Hansen.
   Nucleic Acids Research, 27:370-372, 1999.
  
   More information about the method can be found at:
   
      http://www.cbs.dtu.dk/services/NetOGlyc/


   DOWNLOAD

   NetOGlyc 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?netOglyc

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


   PRE-INSTALLATION

   NetOGlyc 3.1 will run on the most common UNIX platforms e.g. Linux,  SunOS
   etc. The package consists of two files:

        netOglyc-3.1.readme		this file
        netOglyc-3.1.<unix>.tar.Z	compressed TAR archive

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


   INSTALLATION

   1. Uncompress and untar the package:

      cat netOglyc-3.1.<unix>.tar.Z | uncompress | tar xvf -

   This will produce a directory 'netOglyc-3.1'.

   2. In the 'netOglyc-3.1' directory edit the main 'netOglyc' script. In the
   beginning of the script the following variables should be configured:

      GLYCHOME	full path to the netOglyc-3.1 directory		mandatory
      TMP	      "		 temporary directory to use	mandatory
      ECHO	      "		 echo executable		mandatory
      AWK	      "		 awk/nawk/gawk executable	mandatory
      PASTE	      "		 paste executable		mandatory
      GNUPLOT	      "		 gnuplot executable		optional
      PPM2GIF	      "		 ppmtogif executable		optional
      SIGNALP	      "		 signalp executable		optional

   The shell built-in echo command should be avoided as its behaviour differs
   from  platform to platform.  'gnuplot' is needed for NetOGlyc  to generate
   output  graphics.  If GNUPLOT is not set  the '-g' option to NetOGlyc will
   be ignored. If PPM2GIF is not set the '-g' option will generate PostScript
   only.

   SignalP 3.0 is needed for detecting secretory proteins. If it is installed
   the SIGNALP variable should be set.  The intended users of NetOGlyc should
   decide if they need it or not. The NetOGlyc manpage gives more information
   on SignalP.

   3. Test the package:
   
      ./netOglyc test/GLP_MACFU.fsa		# one sequence
      ./netOglyc test/LEUK_RAT.fsa
      ./netOglyc -g test/LEUK_RAT.fsa		# one sequence, graphics
      ./netOglyc -g test/both.fsa		# many sequences, graphics
      mkdir outdir;
      ./netOglyc -g -d outdir test/both.fsa	# as above, custom directory

   The text output of the last command above  should be identical to the file
   'test/both.out';  the 4 graphics files generated should be very similar to
   the PS and GIF files in 'test/'.

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

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

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

      or:

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

   6. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the NetOGlyc method  should be sent
   to Karin Julenius, kj@cbs.dtu.dk.

   CBS, 6 Feb 2007
   K. Rapacki