A Sequential Monte Carlo Method for Motif Discovery

We propose a sequential Monte Carlo (SMC)-based motif discovery algorithm that can efficiently detect motifs in datasets containing a large number of sequences. The statistical distribution of the motifs is modeled by an underlying position weight matrix (PWM), and both the PWM and the positions of the motifs within the sequences are estimated by the SMC algorithm. The proposed SMC motif discovery technique can locate motifs under a number of scenarios, including the single-block model, two-block model with unknown gap length, motifs of unknown lengths, motifs with unknown abundance, and sequences with multiple unique motifs. The accuracy of the SMC motif discovery algorithm is shown to be superior to that of the existing methods based on MCMC or EM algorithms. Furthermore, it is shown that the proposed method can be used to improve the results of existing motif discovery algorithms by using their results as the priors for the SMC algorithm.