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The problem of fast exact and approximate searching for a pattern that contains classes of characters and bounded size gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site is associated with the...
Assigning functions to novel proteins is one of the most important problems in the postgenomic era. Several approaches have been applied to this problem, including the analysis of gene expression patterns, phylogenetic profiles, protein fusions, and protein-protein interactions. In this paper, we...