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Similarity Analysis of DNA Sequences Based on the Relative Entropy

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Advances in Natural Computation (ICNC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3610))

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Abstract

This paper investigates the similarity of two sequences, one of the main issues for fragments clustering and classification when sequencing the genomes of microbial communities directly sampled from natural environment. In this paper, we use the relative entropy as a criterion of similarity of two sequences and discuss its characteristics in DNA sequences. A method for evaluating the relative entropy is presented and applied to the comparison between two sequences. With combination of the relative entropy and the length of variables defined in this paper, the similarity of sequences is easily obtained. The SOM and PCA are applied to cluster subsequences from different genomes. Computer simulations verify that the method works well.

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References

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Shanghai Jiaotong University, 1954 Hua Shan Rd., Shanghai, 200030, China

    Wenlu Yang, Xiongjun Pi & Liqing Zhang

  2. Shanghai Institutes for Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China

    Wenlu Yang & Xiongjun Pi

  3. Department of Electronic Engineering, Shanghai Maritime University, Shanghai, 200135, China

    Wenlu Yang

Authors
  1. Wenlu Yang
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  2. Xiongjun Pi
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  3. Liqing Zhang
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Editor information

Editors and Affiliations

  1. School of Electrical and Electronic Engineering, Nanyang Technological University, Block S1, Nanyang Avenue, 639798, Singapore

    Lipo Wang

  2. School of Software, Sun Yat-Sen University, 510275, Guangzhou, China

    Ke Chen

  3. School of Computer Engineering, Nanyang Technological University, BLK N4, 2b-39, Nanyang Avenue, 639798, Singapore

    Yew Soon Ong

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© 2005 Springer-Verlag Berlin Heidelberg

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Yang, W., Pi, X., Zhang, L. (2005). Similarity Analysis of DNA Sequences Based on the Relative Entropy. In: Wang, L., Chen, K., Ong, Y.S. (eds) Advances in Natural Computation. ICNC 2005. Lecture Notes in Computer Science, vol 3610. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11539087_137

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  • DOI: https://doi.org/10.1007/11539087_137

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28323-2

  • Online ISBN: 978-3-540-31853-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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