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Fast index based algorithms and software for matching position specific scoring matrices

Authors:	Michael Beckstette Robert Homann Robert Giegerich Stefan Kurtz

Institution:	1. International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBITec), Bielefeld University, D-33594, Bielefeld, Germany 2. Technische Fakult?t, Universit?t Bielefeld,, Postfach 100 131, D-33501, Bielefeld, Germany 3. Zentrum für Bioinformatik, Universit?t Hamburg, 20146, Hamburg, Germany

Abstract:	Background 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.

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