SDDA (SDICT) is a program that uses a stochastic dictionary model to search for transcription factor binding sites (motifs) in DNA sequences. The algorithm is capable of detecting multiple motif sites of multiple types, gapped motifs, finding the optimal motif width, and calculating motif significance through a MAP score and the Bayes factor using computational methods.
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Gupta, M. and Liu, J. S. (2003).
Discovery of conserved sequence patterns using a stochastic dictionary model.
Journal of the American Statistical Association 98 (461), 55-66