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International Conference on Discovery Science

DS 2012: Discovery Science pp 81–94Cite as

A Trim Distance between Positions in Nucleotide Sequences

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 7569))

Abstract

In this paper, first we introduce a label-based closest-neighbor trimming method to trim a phylogenetic tree built from nucleotide sequences according to the labels of leaves. Next, by replacing the indices of nucleotide sequences as labels of leaves with the nucleotides occurring in a position, we formulate a trim distance between two positions in nucleotide sequences as the LCA-preserving distance between the trimmed phylogenetic trees according to nucleotides occurring in the positions. Finally, we apply the trim distance to compare pandemic influenza A (H1N1) viruses with non-pandemic ones.

This work is partially supported by Grand-in-Aid for Scientific Research 22240010, 24300060 and 24700289 from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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References

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Author information

Authors and Affiliations

  1. Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, 820-8502, Japan

    Shunsuke Makino & Takaharu Shimada

  2. Department of Artificial Intelligence, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, 820-8502, Japan

    Kouichi Hirata

  3. Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, 526-0829, Japan

    Kouki Yonezawa

  4. Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, North 20 West 10, Kita-ku, Sapporo, 001-0020, Japan

    Kimihito Ito

Authors
  1. Shunsuke Makino
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  2. Takaharu Shimada
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  3. Kouichi Hirata
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  4. Kouki Yonezawa
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  5. Kimihito Ito
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Editor information

Editors and Affiliations

  1. LIP6 laboratory, Parix VI University, 4, place Jussieu, 75005, Paris, France

    Jean-Gabriel Ganascia

  2. Telecom Bretagne, UMR 6285 Lab-STICC, Technopôle Brest-Iroise - CS 83818, 29238, Brest Cedex 3, France

    Philippe Lenca

  3. INSA Lyon, UMR 5205 LIRIS, 7, avenue Jean Capelle, 69621, Villeurbanne Cedex, France

    Jean-Marc Petit

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© 2012 Springer-Verlag Berlin Heidelberg

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Makino, S., Shimada, T., Hirata, K., Yonezawa, K., Ito, K. (2012). A Trim Distance between Positions in Nucleotide Sequences. In: Ganascia, JG., Lenca, P., Petit, JM. (eds) Discovery Science. DS 2012. Lecture Notes in Computer Science(), vol 7569. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33492-4_9

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  • DOI: https://doi.org/10.1007/978-3-642-33492-4_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33491-7

  • Online ISBN: 978-3-642-33492-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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