MixMHC2pred-2.0

Official release of MixMHC2pred-2.0, a pan-allele predictor of MHC-II ligands and CD4+T-cell epitopes.

Release notes are available here.

Current release corresponds to version 2.0.2 (re-tagged here in order to obtain a permanent Zenodo doi from this release).

MixMHC2pred - version 2.0

Release of MixMHC2pred-2.0, a major update of our predictor:

• This new version allows for pan-allele predictions for human and non-human MHC-II alleles. I.e. it now manages to predict the peptide presentation for alleles that are absent from the training data.
• The implementation vastly changed; it is now based on multiple neural networks and it was trained on a much larger MHC-II peptidomics dataset than v1.xx.
• Please note that the format of the input and output files have changed, as well as the available input arguments (please check the README for details of the input/output files and usage).

Release candidate version of MixMHC2pred-2.0

Pre-release version of the major update of MixMHC2pred-2.0.

• This new version allows for pan-allele predictions for human and non-human MHC-II alleles.
• The implementation vastly changed; it is now based on multiple neural networks and it was trained on a much larger MHC-II peptidomics dataset.
• Please note that the format of the input and output files have changed, as well as the available input arguments (see README for details of the input/output files and usage).

MixMHC2pred - version 1.2

New version outputting predictions from each allele and various other changes:

• Output contains now also the individual predictions from each allele in
  addition to the score of the best allele per peptide.
• Outputted core positions correspond now to the P1 of the binding core, counted
  from the N-terminus of the peptide (first amino acid has a value of 1).
• Added a "FAQ" document.
• There is an option to allow having unspecified amino acids in the peptide
  sequence (these should be written as "X" or "-").
• Added the option "--best_s" (see README).
• Slightly updated the %Rank computations, avoiding in general having scores of
  exactly 0, and allowing the predictions for peptides up to a size of 25 amino
  acids.
• Corrected a bug when input file was given in fasta format with multiple lines
  per peptide sequence.

Version 1.1 of MixMHC2pred

Version including nicer readme and other small changes.

Pre-release of MixMHC2pred version 1.1.

v1.1

Version 1.1 of MixMHC2pred

Release of MixMHC2pred version 1.0.

Public release of MixMHC2pred version 1.0.