Journal Article

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

Janne Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas and Esko Ukkonen

in Bioinformatics

Volume 25, issue 23, pages 3181-3182
Published in print December 2009 | ISSN: 1367-4803
Published online September 2009 | e-ISSN: 1460-2059 | DOI:

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Summary: 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 The source code is also available under the terms of a GNU General Public License (GPL).


Journal Article.  1464 words. 

Subjects: Bioinformatics and Computational Biology

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