Harnessing the cellular immune system to the gene-prediction cart

Prediction of genes and verification of their bona fide expression in the cell are major challenges of the post-genomic era. Here, we demonstrate how information from the apparently unrelated field of cellular immunology can be recruited for these challenging tasks. The cellular immune system presents short peptides that are the degradation products of both foreign and self-proteins expressed in the cell. We carried out a comprehensive search comparing these peptides to all accumulated human sequence data. Our findings illustrate how these 'presented self-peptides' are informative for the identification of new genes, for hypothetical gene verification, for verifying gene expression at the protein level and for supporting splice junctions.