
MHC class I peptide binding prediction tools - version 2.17
===========================================================

Introduction
------------
This package contains a collection of prediction tools for peptides binding to 
Major Histocompatibility Complex (MHC) class I molecules. The collection is a 
mixture of pythons scripts and linux 32-bit environment specific binaries.


Prerequisites:
-------------

+ Linux 32-bit environment
  * http://www.ubuntu.com/
    - This distribution has been tested on Linux/Ubuntu 32 bit system.

+ Python 2.7 or higher
  * http://www.python.org/
    - Under ubuntu: sudo apt-get install python2.7

+ tcsh
  * http://www.tcsh.org/Welcome
    - Under ubuntu: sudo apt-get install tcsh

+ gawk
  * http://www.gnu.org/software/gawk/
    - Under ubuntu: sudo apt-get install gawk


Installation:
------------
Unpack the tar.gz files (IEDB_MHC_I-VERSION.tar.gz)
Run the 'configure' script to set up path variables for trained models.

Specifically for mhc_i:
  $ tar -zxvf IEDB_MHC_I-VERSION.tar.gz
  $ cd mhc_i
  $ ./configure

  
Available prediction methods are:
---------------------------------
ann
comblib_sidney2008
consensus
IEDB_recommended
netmhcpan
smm
smmpmbec
pickpocket
netmhccons
netmhcstabpan


Method versions used in the tool:
---------------------------------
ann             4.0
netmhcpan       3.0
pickpocket      1.1
netmhccons      1.1
netmhcstabpan   1.0


Available commands: 
------------------
* List all available commands.
./src/predict_binding.py

* List all available MHC-I prediction methods.
./src/predict_binding.py method

* List all available (MHC,peptide_length) for a given method.
./src/predict_binding.py [method] mhc

* Make predictions given a file containing a list of sequences.
./src/predict_binding.py [method] [mhc] [peptide_length] [input_file]

* Make predictions given a file containing a list of sequences and user-provided MHC sequence.
** Only netmhcpan has this option.
./src/predict_binding.py [method] -m [input_file_mhc] [peptide_length] [input_file]


Example:
--------
* List all alleles for ANN method
./src/predict_binding.py ann mhc

* To use ANN method to predict binding for allele HLA-A*02:01 and length 9 with protein sequence(s) in file input_sequence.fasta
./src/predict_binding.py ann HLA-A*02:01 9 ./examples/input_sequence.fasta

* To use NetMHCpan method to predict binding for user defined MHC protein sequence and length 9 with protein sequence(s) in file input_sequence.fasta
./src/predict_binding.py netmhcpan -m ./examples/protein_mhc_B0702.fasta 9 ./examples/input_sequence.fasta

* You may also redirect (pipe) the input file into the script.
echo -e ./examples/input_sequence.fasta | ./src/predict_binding.py ann HLA-A*02:01 9
echo -e ./examples/input_sequence.fasta | ./src/predict_binding.py netmhcpan -m ./examples/protein_mhc_B0702.fasta 9

* To redirect the output to a file, use:
./src/predict_binding.py smm "HLA-A*02:01" 9 ./examples/input_sequence.fasta > output.txt

