quassi

QUASSI The major histocompatibility complex (MHC), a cell-surface protein mediating immune recognition, plays important roles on immune response system in all higher vertebrates. The polymorphism of MHC in the regions determining the peptide binding specificity complexes MHC molecule classification. Serotype information also provides important evidence for MHC classification. As well known, both protein structure and function are determined by sequence contents, especially at some specific positions which play crucial roles in entire MHC. A 21-residue pseudo sequence was found by Nielson enough to capture the encoded information. Here, we proposed a linear programming based approach called quassi to find significance residue positions as well as quantifying their significance in MHC II DR molecules. ## INPUT ## Input is a string of fasta sequences of MHC II DR molecules. 1284 protein sequences of HLA-DR molecules downloaded from ImMunoGeneTicsHLA database. After removing