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Similarity Searching in DNA Sequences by Spectral Distortion Measures

  • Tuan D. Pham
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4065)

Abstract

Searching for similarity among biological sequences is an important research area of bioinformatics because it can provide insight into the evolutionary and genetic relationships between species that open doors to new scientific discoveries such as drug design and treament. In this paper, we introduce a novel measure of similarity between two biological sequences without the need of alignment. The method is based on the concept of spectral distortion measures developed for signal processing. The proposed method was tested using a set of six DNA sequences taken from Escherichia coli K-12 and Shigella flexneri, and one random sequence. It was further tested with a complex dataset of 40 DNA sequences taken from the GenBank sequence database. The results obtained from the proposed method are found superior to some existing methods for similarity measure of DNA sequences.

Keywords

Markov Chain Model Biological Sequence Distortion Measure Chaos Game Representation Signal Analysis Method 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Tuan D. Pham
    • 1
    • 2
  1. 1.Bioinformatics Applications Research Centre 
  2. 2.School of Information TechnologyJames Cook UniversityTownsvilleAustralia

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