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Title
Fast index based algorithms and software for matching position specific scoring matrices.
Authors
Beckstette, Michael; Homann, Robert; Giegerich, Robert; Kurtz, Stefan
Abstract
In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task.