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Published in:
2007 | OriginalPaper | Chapter
Computing Exact p-Value for Structured Motif
Authors : Jing Zhang, Xi Chen, Ming Li
Published in: Combinatorial Pattern Matching
Publisher: Springer Berlin Heidelberg
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Extracting motifs from a set of DNA sequences is important in computational biology. Occurrence probability is a common used statistics to evaluate the statistical significance of a motif. A main problem is how to calculate the occurrence probability of the motif on the random model of DNA sequence efficiently and accurately. In this paper, we are interested in a particular motif model which is useful in transcription process. This motif, which is called structured motif, is composed two motif words on single nucleotide alphabet and with fixed spacers between them. We present an efficient algorithm to calculate the exact occurrence probability of a structured motif on a given sequence. It is the first non-trivial algorithm to calculate the exact p-value for such kind of motifs.