Version 2.1

MixMHCpred

@@ -1,18 +1,18 @@
 #!/bin/bash
 
 ###############
-# MixMHCpred2.0.2 is a predictor of HLA ligand displayed at the cell surface.
+# MixMHCpred2.1 is a predictor of HLA ligand displayed at the cell surface.
 #
-# MixMHCpred2.0.2 can be used freely by academic groups for non-commercial purposes (see license).
+# MixMHCpred2.1 can be used freely by academic groups for non-commercial purposes (see license).
 # The product is provided free of charge, and, therefore, on an "as is"
 #  basis, without warranty of any kind.
 #
 # FOR-PROFIT USERS
-# If you plan to use MixMHCpred (version 2.0.2) or any data provided with the script in any for-profit
+# If you plan to use MixMHCpred (version 2.1) or any data provided with the script in any for-profit
 # application, you are required to obtain a separate  license.
 # To do so, please contact [email protected] or [email protected] at the Ludwig Institute for  Cancer Research Ltd.
 #
-# If you use MixMHCpred2.0.2 in a publication, please cite:
+# If you use MixMHCpred2.1 in a publication, please cite:
 # Bassani-Sternberg M et al. Deciphering HLA motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity, PLoS Comp Bio (2017).
 # and
 # Gfeller et al. The length distribution and multiple specificity of naturally presented HLA-I ligands, J Immunol (2018).
@@ -43,7 +43,7 @@ usage="Usage: MixMHCpred -i INPUT_FILE -o OUTPUT_FILE -h LIST_OF_ALLELES"
 
 if [[ "$1" == "--help" || "$1" == "-h" ]]; then
 cat <<END
-MixMHCpred2.0.2
+MixMHCpred2.1
 $usage
 Mandatory parameters:
 

README

@@ -1,17 +1,17 @@
 
 ###############
-# MixMHCpred2.0.2 is a predictor of HLA-I ligand displayed at the cell surface.
+# MixMHCpred2.1 is a predictor of HLA-I ligand displayed at the cell surface.
 #
-# MixMHCpred2.0.2 can be used freely by academic groups for non-commercial purposes (see license).
+# MixMHCpred2.1 can be used freely by academic groups for non-commercial purposes (see license).
 # The product is provided free of charge, and, therefore, on an "as is"
 #  basis, without warranty of any kind.
 #
 # FOR-PROFIT USERS
-# If you plan to use MixMHCpred (version 2.0.2) or any data provided with the script in any for-profit
+# If you plan to use MixMHCpred (version 2.1) or any data provided with the script in any for-profit
 # application, you are required to obtain a separate  license.
 # To do so, please contact [email protected] or [email protected] at the Ludwig Institute for  Cancer Research Ltd.
 #
-# If you use MixMHCpred2.0.2 in a publication, please cite:
+# If you use MixMHCpred2.1 in a publication, please cite:
 # Bassani-Sternberg M et al. Deciphering HLA motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity, PLoS Comp Bio (2017).
 # and
 # Gfeller et al. The length distribution and multiple specificity of naturally presented HLA-I ligands, J Immunol (2018).
@@ -22,28 +22,28 @@
 ###############
 
 ########################
-NEW FEATURES OF VERSION 2.0.2
+NEW FEATURES OF VERSION 2.1
 ########################
 
-- Following common practices in NetMHCpan and MixMHC2pred, P-values have been replaced by %Rank (i.e., multiplied by 100). These values correspond to the fraction of random peptides of length 8 to 14 that have a score higher than the one of the peptide for predictions are done.
+- Expanded allelic coverage
 
 ############
 INSTALLATION
 ############
 
 For Mac and Linux:
 
-1) Dowload the MixMHCpred2.0.2.zip file and move it to a directory
+1) Dowload the MixMHCpred2.1.zip file and move it to a directory
 of your choice, where you have writing permissions.
 
-2) Unzip the MixMHCpred2.0.2.zip package.
+2) Unzip the MixMHCpred2.1.zip package.
 
 3) Open the MixMHCpred file and replace lib_path by the
-path to the MixMHCpred2.0.2/lib directory where you have installed the script
+path to the MixMHCpred2.1/lib directory where you have installed the script
 
-4) To run it from anywhere on your computer, add the MixMHCpred2.0.2. directory to your path.
+4) To run it from anywhere on your computer, add the MixMHCpred2.1. directory to your path.
 
-5) To test your installation, make sure you are in the MixMHCpred2.0.2/ directory and run the command (should not take more than a few seconds):
+5) To test your installation, make sure you are in the MixMHCpred2.1/ directory and run the command (should not take more than a few seconds):
 
    ./MixMHCpred -i test/test.fa -o test/out.txt -a A0101,A2501,B0801,B1801
 
@@ -60,7 +60,7 @@ melanoma sample (from Bassani-Sternberg et al. Nat Comm 2016).
 For Linux:
 
 After step 3), you also need to compile the MixMHCpred.cc code. Go to
-MixMHCpred2.0.2/lib and compile with your favorite C++ compiler
+MixMHCpred2.1/lib and compile with your favorite C++ compiler
 (e.g. g++ -O3 MixMHCpred.cc -o MixMHCpred.x)
 
 
@@ -108,10 +108,10 @@ OTHER INFORMATION
   a random sampling of 700,000 peptides from the human proteome (8- to 14-mers).
   This P-value is simply an indicator of how a given peptide scores compares to a universe of random peptides (similar to percentile rank used in other HLA-I ligand predictors). For a single allele, scores larger than 0 correspond to P-values smaller than 0.01.
 
-- The list of alleles is provided in MixMHCpred2.0.2/lib/allele_list.txt.
+- The list of alleles is provided in MixMHCpred2.1/lib/allele_list.txt.
   The third column indicates the number of motifs used to describe the specificity of a given allele and a given peptide length
 
-- The MixMHCpred2.0.2/tmp/ directory is used to store temporary files. Make
+- The MixMHCpred2.1/tmp/ directory is used to store temporary files. Make
   sure there is no restriction for writing and reading files in this directory.
 
 - Predictions of Cystein containing peptides are less reliable due to the low detection rate of Cys in MS.