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13th IEEE International Conference on BioInformatics and BioEngineering (2006)
Arlington, Virginia
Oct. 16, 2006 to Oct. 18, 2006
ISBN: 0-7695-2727-2
pp: 45-52
Di Wang , Northeastern University, Shenyang 110004, China
Guoren Wang , Northeastern University, Shenyang 110004, China
Qingquan Wu , Northeastern University, Shenyang 110004, China
Baichen Chen , Northeastern University, Shenyang 110004, China
Changyong Yu , Northeastern University, Shenyang 110004, China
Yi Zhao , Northeastern University, Shenyang 110004, China
Ge Yu , Northeastern University, Shenyang 110004, China
ABSTRACT
Searching for approximate repetitions in a DNA sequence has been an important topic in gene analysis. One of the problems in the study is that because of the varying lengths of patterns, the similarity between patterns cannot be judged accurately if we use only the concept of ED ( Edit Distance ). In this paper we shall use the function Similar to compute similarity, which considers both the difference and sameness between patterns at the same time. Seeing the computational complexity, we shall also propose a new distance PFD ( Partition Frequency Distance ) and design a new filter based on PFD, with which we can sort out candidate set of approximate repetitions efficiently. We use SUA instead of sliding window to get the fragments in a DNA sequence, so that the patterns of an approximate repetition have no limitation on length. The results show that with this technique we are able to find a bigger number of approximate repetitions than that of those found with tandem repeat finder.
INDEX TERMS
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CITATION

C. Yu et al., "Partition Frequency Distance based Filter Method for Finding Approximate Repetitions in DNA Sequences," 13th IEEE International Conference on BioInformatics and BioEngineering(BIBE), Arlington, Virginia, 2006, pp. 45-52.
doi:10.1109/BIBE.2006.253314
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