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. 2009 Dec 1;25(23):3181-2.
doi: 10.1093/bioinformatics/btp554. Epub 2009 Sep 22.

MOODS: fast search for position weight matrix matches in DNA sequences

Janne Korhonen  1 , Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen
Affiliations

MOODS: fast search for position weight matrix matches in DNA sequences

Janne Korhonen et al. Bioinformatics. .

Abstract

MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library.

Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).

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