NetStart 1.0		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   NetStart   predicts   translation   start  in  nucleotide  sequences  from
   vertebrates and  dicot plants  (e.g. Arabidopsis thaliana)  using a neural
   network  approach.  The method is  described  in detail  in  the following
   article:

   Neural network prediction of translation initiation sites in eukaryotes: 
   perspectives for EST and genome analysis.
   A. G. Pedersen  and  H. Nielsen.
   ISMB 5, 226-233, 1997.

   More information about the method can be found at:

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


   DOWNLOAD

   The NetStart 1.0 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?netstart

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


   PRE-INSTALLATION

   NetStart 1.0 will run on the most common UNIX platforms e.g.  Linux, SunOS
   etc. The package consists of two files:
  
       netstart-1.0.readme          this file
       netstart-1.0.<unix>.tar.Z    compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install. After
   installation NetStart will occupy around 1.8 Mb of disk space.


   INSTALLATION

   1. Uncompress and untar the package:

      cat netstart-1.0c.tar.Z | uncompress | tar xvf -

   This will produce a directory 'netstart-1.0c'.

   2. In 'netstart-1.0c' locate and edit  the main script 'netstart'.  In the
   beginning of the script the following variables should be configured:

      NSHOME	full path to the netstart-1.0c directory (mandatory)
      AWK	      "      awk/nawk/gawk executable
      ECHO	      "      'echo' executable

   The shell built-in echo command should be avoided as its behaviour differs
   from platform to platform.

   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:

      ./netstart -at test/at.fsa

   Compare  the output  to  the contents of the file 'test/at.fsa.out'.  They
   should be identical. If there is only one line of output:
   
      Translation start predictions for ...

   increase the swap space on the machine and test again.

   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 scientific aspects of the NetStart method  should be sent to:

      Anders Gorm Pedersen, gorm@cbs.dtu.dk
      Soeren Brunak, brunak@cbs.dtu.dk

   CBS, 5 Mar 2007
   K. Rapacki