YinOYang 1.2		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   YinOYang 1.2 produces predictions of  O-(beta)-GlcNAc  attachment sites in
   eukaryotic protein sequences using artificial neural networks. It can also
   use NetPhos,  to mark possible phosphorylated sites and hence identify the
   "Yin-Yang" sites.  Such sites  may be modified  reversibly and dynamically
   by O-GlcNAc or phosphate groups at different times in the cell. The method
   is described in detail in the references:

   Prediction of glycosylation  sites  in proteomes:  from post-translational
   modifications to protein function.
   R Gupta.
   Ph.D. thesis at CBS, 2001.

   Prediction of glycosylation across the human proteome  and the correlation
   to protein function.
   Gupta, R. and S. Brunak.
   Pacific Symposium on Biocomputing, 7:310-322, 2002.

   The NetPhos method is described in:

   "Sequence and structure-based prediction of eukaryotic protein
   phosphorylation sites".
   N. Blom, S. Gammeltoft and S. Brunak.
   J Mol Biol. 294(5): 1351-1362, 1999.

   More information on both methods can be found at:

       http://www.cbs.dtu.dk/services/YinOYang/
       http://www.cbs.dtu.dk/services/NetPhos/


   DOWNLOAD

   The YinOYang 1.2 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?yinOyang

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


   PRE-INSTALLATION

   YinOYang 1.2 will run on the most common UNIX platforms e.g.  Linux, SunOS
   etc. The package consists of two files:
  
       yinOyang-1.2.readme		this file
       yinOyang-1.2.<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 YinOYang-1.2.<unix.tar.Z | uncompress | tar xvf -

   This will produce a directory 'yinOyang-1.2'.

   2. In the 'yinOyang-1.2' directory edit the main 'yinOyang' script. In the
   beginning of the script the following variables should be configured:

      YYHOME	full path to the yinOyang-1.2 directory		mandatory
      ECHO	      "		 echo executable		mandatory
      AWK	      "		 awk/nawk/gawk executable	mandatory
      PERL	      "		 perl executable		mandatory
      GETSPROT	      "		 Swiss-Prot browser		optional
      GNUPLOT	      "		 gnuplot executable		optional
      PPM2GIF	      "		 ppmtogif executable		optional
      SIGNALP	      "		 signalp executable		optional
      NETPHOS         "          netphos executable		optional*

   The shell built-in echo command should be avoided  as its behavior differs
   from platform to platform.  AWK and PERL are used by a number of auxiliary
   scripts called by YinOYang.
   
   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 YinOYang to generate output  graphics. If GNUPLOT is
   not set the '-g' option to YinOYang will be ignored. If PPM2GIF is not set
   the '-g' option will generate PostScript only.

   SIGNALP 3.0 is needed for detecting secretory proteins.
   
   NETPHOS 2.0 is used by YinOYang for prediction of phosphorylation. Without
   it the '-y' option does not work and Yin-Yang predictions cannot be made.

   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:
   
      ./yinOyang test/LEUK_RAT.fsa		# one sequence
      ./yinOyang -y test/LEUK_RAT.fsa		# one sequence, Yin-Yang pred
      ./yinOyang -y test/CBG_HUMAN.fsa
      ./yinOyang -y -g test/LEUK_RAT.fsa	# one sequence, graphics
      ./yinOyang -y -g test/two.fsa		# many sequences, graphics
      ./yinOyang -y -i LEUK_RAT			# input from Swiss-Prot entry

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

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

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

      or:

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

7. Enjoy ...


   PROBLEMS

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

   CBS, 12 Feb 2007
   K. Rapacki