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Selection of proteins for human MHC class II presentation.

We investigated the predicted function of proteins eluded from human MHC class II molecules. Peptides that are presented by MHC class II were obtained from the SYFPEITHI database and the corresponding proteins were found in the SWISSPROT database. The functions of these proteins were predicted using the protfun server. Our analysis showed that human proteins presented by MHC class II molecules are likely to be in the cell envelope, be a receptor or involved in immune responses. Presented proteins from bacteria and virus, on the other hand, are more likely to be involved in regulatory functions, translation, transcription as well as replication. These results can lead to better understanding the autoimmunity and the response to infections.