Motif Occurrence Detection Suite for matching position weight matrices (PWMs) against DNA sequences. These tools can handle PWMs containing dependencies among adjacent positions, such as SNPs, insertions, and deletions. It can be as a standalone analysis tool or a component other programs.
Computational biology, Sequence sites, features and motifs
Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E "MOODS: fast search for position weight matrix matches in DNA sequences." Bioinformatics 2009; 25(23):3181-2 https://doi.org/10.1093/bioinformatics/btp554
PMID: 19773334
PMCID: PMC2778336
Korhonen JH, Palin K, Taipale J, Ukkonen E "Fast motif matching revisited: high-order PWMs, SNPs and indels." Bioinformatics 2017; 33(4):514-521 https://doi.org/10.1093/bioinformatics/btw683
PMID: 28011774
Cinzia Pizzi, Pasi Rastas and Eesko Ukkonen "Finding Significant Matches of Position Weight Matrices in Linear Time." IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(1), pages 69 - 79. (2011) https://doi.org/10.1109/TCBB.2009.35
PMID: 21071798
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