mhcmatch

Peptide–MHC presentation, cross-reactivity, and motif tools on the seqtree fuzzy-search substrate. mhcmatch productionizes the reference seqtree.pmhc methodology and adds a pseudosequence-based cross-allele diffusion model that rescues rare alleles by borrowing from groove-similar frequent ones.

The mathematical and statistical theory lives in the technical appendix (appendix/mhcmatch.tex); the development plan is in ROADMAP.md.

Getting Started

Install, build a store, predict restriction, scan a protein.

API Reference

Store, search, proteome, pseudoseq diffusion, logos.

Capabilities

• Restriction & presentation — rank presenting alleles for a peptide (single / set / all, human & mouse), flag non-binders, scan a protein for presented peptides.

• Large-scale similarity — find similar peptides across big sets / proteomes by same-MHC binding or TCR-facing recognition; neoantigen molecular mimicry with per-allele E-values.

• Anchor / TCR-facing split — decompose a peptide into anchor and TCR-facing parts.

• Near-exact source lookup — find the self peptide a neoantigen derives from.

• Motif logos — per-allele information-content logos with length distributions.

• Pseudosequence diffusion — allele similarity, clustering, and kernel-shrinkage pooling that rescues rare alleles (anchor-factored, with learned per-pocket groove weights).