Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)
Discovery of Repetitive Patterns in DNA with Accurate Boundaries
Minneapolis, Minnesota
October 19-October 21
ISBN: 0-7695-2476-1
DOI Bookmark:
http://doi.ieeecomputersociety.org/10.1109/BIBE.2005.23
The accurate identification of repeats remains a challenging open problem in bioinformatics. Most existing methods of repeat identification either depend on annotated repeat databases or restrict repeats to pairs of similar sequences that are maximal in length. The fundamental flaw in most of the available methods is the lack of a definition that correctly balances the importance of the length and the frequency. In this paper, we propose a new definition of repeats that satisfies both criteria. We give a novel characterization of the building blocks of repeats, called elementary repeats, which leads to a natural definition of repeat boundaries. We design efficient algorithms and test them on synthetic and real biological data. Experimental results show that our method is highly accurate.
Citation:
Jie Zheng, Stefano Lonardi, "Discovery of Repetitive Patterns in DNA with Accurate Boundaries," bibe, pp.105-112, Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05), 2005
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