title: Mining poly-regions in DNA.
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.
authors.affiliation: Department of Information and Computer Science, Aalto University 00076, Finland. panagiotis.papapetrou@tkk.fi
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Papapetrou
authors.forename: Gary
authors.initials: G
authors.lastname: Benson
authors.forename: George
authors.initials: G
authors.lastname: Kollios
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA