Efficient methods for generating optimal single and multiple spaced seeds

Biologists highly rely on good algorithms for finding homologous regions in bimolecular sequences. An advanced homology search program named PatternHunter has recently been developed, unlike the well-known program BLAST using a consecutive model, it utilizes a spaced seed model to attain higher sensitivity. We have developed a new program, which extends PatternHunter from a single spaced model to a multiple spaced model. In this paper, we describe methods for finding optimal single and multiple spaced models.