Bayesian Unsupervised Learning of DNA Regulatory Binding Regions.pdfVIP

Hindawi Publishing Corporation Advances in Artificial Intelligence Volume 2009, Article ID 219743, 11 pages doi:10.1155/2009/219743 Research Article Bayesian Unsupervised Learning of DNA Regulatory Binding Regions Jukka Corander,1 Magnus Ekdahl,2 and Timo Koski3 1 ˚ Department of Mathematics, Abo Akademi University, 20500 Turku, Finland 2 Department of Mathematics, University of Linkoping, 58183 Linkoping, Sweden ¨ ¨ 3 Department of Mathematics, The Royal Institute of Technology, 100 44 Stockholm, Sweden Correspondence should be addressed to Jukka Corander, jukka.corander@abo.fi Received 13 February 2009; Revised 6 June 2009; Accepted 2 July 2009 Recommended by Djamel Bouchaffra Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either scan for previously known motif types or to attempt de novo identification of a fixed number (typically one) of putative motifs. Most approaches assume the existence of reliable biodatabase information to build probabilistic a priori description of the motif classes. Examples of attempts to do probabilistic unsupervised learning about the number of putative de novo motif types and their positions within a set of DNA sequences are very rare in the literature. Here we show how such a learning problem can be formulated using a Bayesian model that targets to simultaneously maximize the marginal likelihood of sequence data arising under multiple motif types as well as under the background DNA model, which equ