International Conference on Information Technology and Computer Science, 3rd (ITCS 2011)
12 Position Dependencies among Multinomial Distribution for Motif Discovery Based on Gibbs Sampling
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Motif discovery of DNA sequences is a key problem in Bioinformatics. Recent biological experiments show that there exists dependency among positions in some motifs significantly. A Gibbs sampling based algorithm, which considers position dependencies among multinomial distributions, is presented in this paper. The implementation of this approach is named SimiMotif. SimiMotif uses chi-square test or Fisher's exact test to determine the dependence among positions of a motif which described as a position frequency matrices. SimiMotif is capable of discovering several different motifs with differing numbers of occurrences per sequence. SimiMotif is tested on benchmarks of Tompa et al. and Sandve et al.. The test results are compared with several existing methods, and it is shown that SimiMotif is feasible and effective.