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    Mining poly-regions in DNA

    Papapetrou, Panagiotis and Benson, G. and Kollios, G. (2012) Mining poly-regions in DNA. International Journal of Data Mining and Bioinformatics 6 (4), p. 406. ISSN 1748-5673.

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    Abstract

    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.

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): DNA polyregions, burstiness, sliding windows, recursive segmentation, majority vote, nucleosomes, bursty DNA, DNA sequences, bioinformatics, arrangement mining, data mining
    School: Birkbeck Schools and Departments > School of Business, Economics & Informatics > Computer Science and Information Systems
    Depositing User: Sarah Hall
    Date Deposited: 26 Jul 2013 10:37
    Last Modified: 26 Jul 2013 10:37
    URI: http://eprints.bbk.ac.uk/id/eprint/7847

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