- Definition files of the alleles are not tracked on github anymore but can be downloaded from http://mixmhc2pred.gfellerlab.org/PWMdef, including alleles from multiple species.
- Added the option
-eto output intermediate scores in addition to the final %Rank.
- Release of MixMHC2pred-v2.0 (as full version, not RC version anymore).
- No major change with respect to the 2.0.RC (see news of 10.06.2022). It was only retrained after minor changes on the training data used.
- Major update of MixMHC2pred, allowing for pan-allele predictions for human and non-human MHC-II alleles.
- 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.
- 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.
- Public release of MixMHC2pred accompanying the Nature Biotechnology paper.
- Public release of MixMHC2pred accompanying our bioRxiv preprint.