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Mining poly-regions in DNA
Stockholm University, Faculty of Social Sciences, Department of Computer and Systems Sciences.
2012 (English)In: International journal on data mining and bioinformatics, ISSN 1748-5673, Vol. 6, no 4, 406-428 p.Article in journal (Refereed) Published
Abstract [en]

We study the problem of mining poly-regions in DNA. A poly-region is defined as a bursty DNA area, i.e., area of elevated frequency of a DNA pattern. We introduce a general formulation that covers a range of meaningful types of poly-regions and develop three efficient detection methods. The first applies recursive segmentation and is entropy-based. The second uses a set of sliding windows that summarize each sequence segment using several statistics. Finally, the third employs a technique based on majority vote. The proposed algorithms are tested on DNA sequences of four different organisms in terms of recall and runtime.

Place, publisher, year, edition, pages
InderScience Publishers, 2012. Vol. 6, no 4, 406-428 p.
National Category
Information Systems
Research subject
Computer and Systems Sciences
URN: urn:nbn:se:su:diva-100729DOI: 10.1504/IJDMB.2012.049278OAI: diva2:695737
Available from: 2014-02-12 Created: 2014-02-12 Last updated: 2014-04-22Bibliographically approved

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Papapetrou, Panagiotis
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