NetMHCpan 2.4              INSTALLATION INSTRUCTIONS


   DESCRIPTION

   The NetMHCpan 2.4 software predicts  binding of peptides  to any known MHC
   molecule using artificial neural networks (ANNs). The method is trained on
   around 115,000 quantitative binding data  covering more than 120 different
   MHC molecules.  Predictions can be made for  HLA-A, B, C, E and G alleles,
   as well as for non-human primates, mouse, cattle and pig.  Furthermore, it
   is also possible to upload full length MHC protein sequences, and have the
   server predict MHC restricted peptides from any given protein of interest.
   The current version  has been retrained  on an extented data set including
   several HLA-C, and two BoLA alleles.  The method is described in detail in
   the following articles:

   Ver. 2.3:
   
   NetMHCpan - MHC class I binding prediction beyond humans.
   Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen,
   Ole Lund, Soren Buus, and Morten Nielsen.
   Immunogenetics. 61(1):1-13, Jan 2009; Epub Nov 12, 2008.
   
   The original paper:

   NetMHCpan, a Method for Quantitative Predictions of Peptide Binding
   to Any HLA-A and -B Locus Protein of Known Sequence.
   Nielsen M, et al.
   PLoS ONE 2(8): e796. doi:10.1371/journal.pone.0000796, 2007.

   More information about the method can be found at:
   
      http://www.cbs.dtu.dk/services/NetMHCpan/


   DOWNLOAD

   The netMHCpan 2.4 software 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?netMHCpan

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


   PRE-INSTALLATION

   netMHCpan 2.4 currently runs under  Darwin (MacOSX), IRIX (SGI) and Linux.
   The package consists of two files:
  
      netMHCpan-2.4.readme         this file
      netMHCpan-2.4.<unix>.tar.Z   compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install. After
   installation the software will occupy less than 8 Mb of diskspace.


   INSTALLATION

   1. Uncompress and untar the package:

      cat netMHCpan-2.4.<unix>.tar.Z | uncompress | tar xvf -

      This will produce a directory 'netMHCpan-2.4'.

   2. From the CBS WWW site download the file:

      http://www.cbs.dtu.dk/services/NetMHCpan-2.4/data.tar.gz

      It should be 6266413 bytes. Put it in the 'netMHCpan-2.4' directory and
      then gunzip and untar it:
      
      gunzip -c data.tar.gz | tar xvf -

      This will produce a directory 'data' (~35MB).  It is necessary  for the
      NetMHCpan 2.4 software to operate;  once it is installed you may delete
      the 'data.tar.gz' file; it will not be needed.


   2. In the 'netMHCpan-2.4' directory edit the script 'netMHCpan':
   
      a. At the top of the file  locate the part labelled  "GENERAL SETTINGS:
         CUSTOMIZE TO YOUR SITE"  and set  the 'NMHOME' variable  to the full
	 path to the 'netMHCpan-2.4' directory on your system;

      b. Set TMPDIR to the full path to the tmp directory of you choice (must
         be user writable);

   3. In the 'netMHCpan-2.4/test' directory test the software:

      > ../netMHCpan -p test.pep > test.pep.myout
      > ../netMHCpan test.fsa > test.fsa.myout
      > ../netMHCpan -hlaseq B0702.fsa test.fsa > test.fsa_userMHC.myout

      The resulting ".myout" files  should not differ  from the corresponding
      ".out" files provided in the package  other than in the directory names
      rounding errors.

   4. Finish the installation:

      a. Copy or link the 'netMHCpan' file to a directory in the users' path.

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

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

         or:

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

   5. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the netMHCpan method should be sent
   to dr Morten Nielsen, mniel@cbs.dtu.dk.

   CBS, 5 Apr 2011
   K. Rapacki