To discover DNA motifs on PBM data, a computational pipeline using Hidden Markov Model (HMM) has been proposed and named, kmerHMM. The method has been compared with the state-of-the-arts methods on well-studied datasets. The results demonstrated the effectiveness of the proposed approach. In addition, belief propagations have been applied to reveal its multimodal motif discovery ability validated by wet-lab experiments.
The Zhang Lab, University of Toronto
- R package /MatLab
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Nucleic Acids Res. 2013 Sep;41(16):e153. doi: 10.1093/nar/gkt574. Epub 2013 Jun 29.
DNA motif elucidation using belief propagation.
Wong KC1, Chan TM, Peng C, Li Y, Zhang Z.