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