MOODS ( MOtif Occurrence Detection Suite) is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds.
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J. Korhonen, P. Martinm?ki, C. Pizzi, P. Rastas and E. Ukkonen.
MOODS: fast search for position weight matrix matches in DNA sequences.
Bioinformatics 25(23), pages 3181-3182. (2009)