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Bioinformatics Advance Access originally published online on September 22, 2009
Bioinformatics 2009 25(23):3181-3182; doi:10.1093/bioinformatics/btp554
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Janne Korhonen 1,*, Petri Martinmäki 1, Cinzia Pizzi 2, Pasi Rastas 1 and Esko Ukkonen 1

1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy

* To whom correspondence should be addressed.


  Abstract

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 http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).

Contact: janne.h.korhonen{at}helsinki.fi

Associate Editor: Alex Bateman

Received on July 14, 2009; revised on September 3, 2009; accepted on September 15, 2009

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