NetPhos 3.1		INSTALLATION INSTRUCTIONS


  DESCRIPTION

  NetPhos  predicts  serine, threonine or tyrosine  phosphorylation  sites  in
  eukaryotic proteins using ensembles of neural networks. Both kinase specific
  and generic predictions are performed.  The method is described in detail in
  the following articles:

  Kinase specific predictions:

  Prediction of post-translational glycosylation and phosphorylation
  of proteins from the amino acid sequence.
  Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S.
  Proteomics. 4(6):1633-49. Review, 2004.

  Generic predictions:

  Sequence and structure-based prediction of eukaryotic protein
  phosphorylation sites.
  Blom N, Gammeltoft S, Brunak S.
  J Mol Biol. 294(5):1351-62, 1999.

  More information about the method can be found at:

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

  DOWNLOAD

  The NETPHOS software package is a property of Center for Biological Sequence
  Analysis. It may be downloaded only after a special agreement.  For academic
  users there is a download site at:

       http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netphos

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


  PRE-INSTALLATION

  NetPhos 3.1 will run on the most common UNIX platforms e.g. Linux, SunOS etc
  The package consists of two files:
  
       netphos-3.1.readme	 this file
       netphos-3.1.<unix>.tar.Z	 compressed TAR archive

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


  INSTALLATION

  The size of the package after installation will not exceed 5 MB.

  1. Decide where you intend to keep the NetPhos 3.1 software.  Uncompress and
     untar the package in that location:

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

     This will produce a directory 'ape-1.0'. APE (All Prediction Environment)
     is an execution environment developed at CBS for prediction methods based
     on neural networks operating on biological sequences. You will be able to
     use it later for other CBS-made softwares.

  2. In the 'ape-1.0' directory  edit the tcsh script 'ape'.  In the paragraph
     labeled  "GENERAL SETTINGS, CUSTOMIZE" at the top of the script customize
     the settings of the following variables to fit your system:

     APE	full path to the 'ape-1.0' directory
     UNIX	the output of "uname -s" e.g. 'Linux' or 'SunOS'
     ARCH	the output of "uname -m" e.g. 'i686' or 'IP35'
     TMP	full path to the temporary directory (must be writable)
     MAXCPU	not used by NetPhos 3.1
     ECHO	full path to the 'echo' executable (not shell built-in)
     AWK	full path to the 'awk' executable (preferably gawk)
     PERL	not used by NetPhos 3.1
     PYTHON	not used by NetPhos 3.1

     GNUPLOT	full path to the 'gnuplot' executable (3.7 or higher)
     PPM2GIF	full path to the 'ppm2gif' executable

  The last two variables  need to be set if you intend to use the  '-g' option
  (graphics, see the manual page).

  You might need to modify the settings after the testing.

  3. Still in the 'ape-1.0' directory test the software  on the test sequences
     shipped with the package:

     > ln -s ape netphos-3.1
     > ./netphos-3.1 test/netphos.P53_HUMAN.fsa		# text output
     > ./netphos-3.1 -g test/netphos.P53_HUMAN.fsa	# text and graphics

     The text output you get should be identical to the file:

     test/netphos-<ver>.P53_HUMAN.out

     shipped with the package.  '<ver>' is the version of the NetPhos software
     (3.1a, Sep 2005).  The file 'netphos-<ver>.P53_HUMAN.gif'  generated with
     the '-g' option should be very similar to the file:

     test/netphos-<ver>.P53_HUMAN.gif
     
     If error messages appear instead  go back to 2) above  and try to correct
     the variable settings  in the 'ape' script.  You might also like  to test
     the other command line options  described on the manual page (see below).

     The sequences in  'test/'  have been extracted from the UniProt database,
     EFTU_HUMAN and P53_HUMAN, respectively.

  4. When you are satisfied that the software works as intended link the 'ape'
     script to a directory in the users' path:

     > cd <some_bin>
     > ln -s <some_location>/ape-1.0/ape ./netphos-3.1
     > ln -s netphos-3.1 netphos

     and test the software again using an ordinary user's identity.

  5. Copy the file  'doc/netphos.1' or 'doc/netphos.Z'  to a suitable location
     in your manual system.


  PROBLEMS
   
  In case of technical problems (with installation, testing, bugs etc.) please
  contact packages@cbs.dtu.dk.

  Questions on the scientific aspects of the NetPhos method  should be sent to
  dr Nikolaj Blom, nikob@cbs.dtu.dk.

  CBS, 6 Feb 2007	K. Rapacki