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


BACKGROUND
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).
Korhonen
Janne
J
Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland. janne.h.korhonen@helsinki.fi
Martinmäki
Petri
P
Pizzi
Cinzia
C
Rastas
Pasi
P
Ukkonen
Esko
E
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D056510:Position-Specific Scoring Matrices; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software