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MOODS: fast search for position weight matrix matches in DNA sequences
Janne Korhonen1, Petri Martinmäki, Cinzia Pizzi
1Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland. janne.h.korhonen@helsinki.fi
Unlabelled:
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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