EXMOTIF efficient structured motif extraction.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access EXMOTIF: efficient structured motif extraction Yongqiang Zhang and Mohammed J Zaki* Address: Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York 12180, USA Email: Yongqiang Zhang - zhangy0@; Mohammed J Zaki* - zaki@ * Corresponding author Published: 16 November 2006 Received: 23 July 2006 Accepted: 16 November 2006 Algorithms for Molecular Biology 2006, 1:21 doi:10.1186/1748-7188-1-21 This article is available from: /content/1/1/21 ? 2006 Zhang and Zaki; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Potential applications of our method include the extraction of single/composite regulatory binding sites in DNA sequences. Results: EXMOTIF is efficient in terms of both time and space and is shown empirically to outperform RISO, a state-of-the-art algorithm. It is also successful in finding potential single/ composite transcription factor binding sites. Conclusion: EXMOTIF is a useful and efficient tool in discovering structured motifs, especially in DNA sequences. The algorithm is available as open-source at: /~zaki/ software/exMotif/ . Introduction characters), 11 positions long. If variable gaps are allowed in a motif, it is called a structured motif. A structured motif can be regarde