MHC class II peptide binding prediction tools - version 3.1.12
=============================================

Release Note
------------
2024-01-22
add methods NetMHCIIpan 4.2 and NetMHCIIpan 4.3
2023-09-19
Two IEDB recommended methods now exist, one for the prediction of peptide binding and one for the prediction of epitopes.
2023-08-25
Update tests
2023-07-21
Add 6 mouse alleles for NetMHCIIpan 4.1
2023-01-20
update NetMHCIIpan 4.0 to NetMHCIIpan 4.1
2022-11-29
update binaries for patching vulnerabilities for NetMHCpan and nn_align
2021-09-03
* update for Debian 10/11
2021-07-27
* remove BoLA alleles from the list for NetMHCIIpan
2021-06-23
* update the available alleles information for the help command
2021-05-19
* remove 'adjusted rank' for NetMHCIIpan 4.0 
2021-01-20
* fix an issue for peptide sequences shorter than 15
2021-01-05
* Fix a minor issue with the NetMHCIIpan 4.0 and percentile rank
2020-09-30
* Update for adding a new version of prediction method NetMHCIIpan 4.0 (BA and EL).
2020-07-29
* Fix an issue regarding method IEDB_recommended fails predicting for some alleles.
2020-05-12
* This release will run only under Python 3.6 or higher.

Introduction
------------
The distributions 'IEDB_MHC_II-3.1.12.tar.gz'contain a collection of peptide binding prediction tools for Major Histocompatibility Complex (MHC) class II molecules.
The collection is a mixture of pythons scripts and linux 64-bit environment specific binaries.

Prerequisites:
-------------
+ Linux 64-bit environment
  * http://www.ubuntu.com/
    - This distribution has been tested on Linux/Ubuntu 64 bit system.

+ Python 3.6 or higher
  * http://www.python.org/

+ 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

+ Perl Env
  * http://perldoc.perl.org/Env.html 
    - Under Redhat/CentOS: sudo yum install perl-Env. 

Installation:
------------
Unpack the tar.gz files (IEDB_MHC_II-3.1.12.tar.gz)
Run the 'configure' script to set up path variables for trained models.

Specifically for mhc_ii:
  $ tar -zxvf IEDB_MHC_II-3.1.12.tar.gz
  $ cd mhc_ii
  $ ./configure.py  
  

Available Methods and versions in the tool:
---------------------------------
consensus3            2.22
NetMHCIIpan EL (IEDB_recommended_epitope)       4.1
NetMHCIIpan BA (IEDB_recommended_binding)       4.1
NetMHCIIpan EL 4.3
NetMHCIIpan BA 4.3
NetMHCIIpan EL 4.2
NetMHCIIpan BA 4.2
nn_align (netmhcii)   2.3
smm_align (netmhcii)  1.1
sturniolo             1.0
comblib               1.0


Available commands: 
------------------
* List all available commands.
python mhc_II_binding.py

* List all available mhc_II prediction methods.
python mhc_II_binding.py method

* List all alleles.
python mhc_II_binding.py allele

* Make predictions given a file containing a list of sequences.
python mhc_II_binding.py [prediction_method] [allele] [input_sequence_file_name]

* Make predictions given a file containing a list of sequences and mutiple alleles.
python mhc_II_binding.py [prediction_method] [allele1,allele2,allele3...] [input_sequence_file_name]

* Make predictions with given peptide lengths. (input length should be between 11 to 30)
python mhc_II_binding.py [prediction_method] [allele] [input_sequence_file_name [lengths]

Example:
--------
* To use Consensus method to predict binding for HLA-DRB1*03:01 with protein sequences in file test.fasta and default peptide length "15"
python mhc_II_binding.py consensus3 HLA-DRB1*03:01 test.fasta

* To use nn_align method to predict binding for HLA-DRB1*01:01 and HLA-DRB1*03:01 with protein sequences in file test.fasta
python mhc_II_binding.py nn_align HLA-DRB1*01:01,HLA-DRB1*03:01 test.fasta

* To have length input other than default value "15"
python mhc_II_binding.py consensus3 HLA-DRB1*03:01 test.fasta 12-15,18

* You may also redirect (pipe) the input file into the script.
echo -e test.fasta | python mhc_II_binding.py consensus3 HLA-DRB1*03:01

* To redirect the output to a file, use:
python mhc_II_binding.py consensus3 HLA-DRB1*03:01 test.fasta > output.txt