T-cell epitope databases and algorithms

The most difficult problem in the study of T-Cells is to figure out

1. which peptides are displayed by the cell and
2. which T-Cell receptor binds to which peptide

Databases of peptides:

• HSPV: Big list of peptides derived from RefSeq and dbSNP, not annotated at all. Downloadable as a fasta file.
• Ludwig CancerImmunomeDB: database of cDNA clones and cancer type, some are annotated to react to serum. Not downloadable.
• Cancer Immunity Peptide list: curated from papers, annotated with cancer, HLA and paper. Easy to scrape.
• TADB: Not online anymore?

Algorithms to predict which peptides are displayed:

• SYFPEITHI - proprietory
• NetMHC - downloadable