NetNGlyc 1.0		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   NetNGlyc predicts N-glycosylation sites in human proteins using artificial
   neural networks. The method is described in detail in the reference:

   Prediction of N-glycosylation sites in human proteins.
   R. Gupta, E. Jung and S. Brunak.
   In preparation, 2011.

   More information on the method can be found at:

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


   DOWNLOAD

   NetNGlyc 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?netNglyc

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


   PRE-INSTALLATION

   NetNGlyc 1.0 will run on the most common UNIX platforms e.g. Linux,  SunOS
   etc. The package consists of two files:

        netNglyc-1.0.readme		this file
        netNglyc-1.0.<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 netNglyc-1.0.tar.Z | uncompress | tar xvf -

   This will produce a directory 'netNglyc-1.0'.

   2. In the 'netNglyc-1.0' directory edit the main 'netNglyc' script. In the
   beginning of the script the following variables should be configured:

      GLYCHOME	full path to the NetNlyc-1.0 directory		mandatory
      AWK	      "		 awk/nawk/gawk executable	mandatory
      PERL	      "		 perl executable		mandatory
      ECHO	      "		 echo executable		mandatory
      GETSPROT	      "		 SWISS-PROT browser		optional
      SIGNALP	      "		 signalp executable		optional
      GNUPLOT	      "		 gnuplot executable		optional
      PPM2GIF	      "		 ppmtogif executable		optional

   AWK and PERL are used by a number of auxiliary scripts called by netNglyc.
   The shell built-in echo command should be avoided  as its behavior differs
   from platform to platform.
   
   If a command-line  SWISS-PROT browser is available on your system GETSPROT
   should be set; otherwise not.  The browser should dump  SWISS-PROT entries
   to standard output; the synopsis should be:

      prog <SWISS-PROT ID>	e.g. "prog LEUK_RAT"

   GNUPLOT is needed for NetNGlyc to generate output  graphics. If GNUPLOT is
   not set the '-g' option to NetNGlyc will be ignored. If PPM2GIF is not set
   the '-g' option will generate PostScript only.

   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:
   
      ./netNglyc test/LEUK_RAT.fsa		# one sequence
      ./netNglyc test/CBG_HUMAN.fsa
      ./netNglyc -g test/LEUK_RAT.fsa		# one sequence, graphics
      ./netNglyc -g test/two.fsa		# many sequences, graphics
      ./netNglyc -i LEUK_RAT			# input from SWISS-PROT

   5. Install  the executable and  the manpage using  the provided  makefile.
   Edit the BINDIR and MANDIR variables to taste and type:
   
      make install
      make install.man

   If you need compiled manpages you should choose 'installc.man'  instead of
   'install.man'.


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the NetNGlyc method  should be sent
   to Ramneek Gupta, ramneek@cbs.dtu.dk.

   CBS, 6 Feb 2007
   K. Rapacki