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Modified PrefixSpan Method for Motif Discovery in Sequence Databases

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PRICAI 2002: Trends in Artificial Intelligence (PRICAI 2002)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 2417))

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Abstract

We propose a motif discovery system that uses a modified PrefixSpan method to extract frequent patterns from an annotated sequence database that has such attributes as a sequence identifier (sequence-id), a sequence, and a set of items. The annotations are represented as the set of items in the database. Frequent sequence patterns and frequent item patterns are extracted from the annotated sequence database. Frequent sequence patterns are located in both identical and non-identical positions among those sequences. In general, the existing PrefixSpan method can extract a large number of identical patterns from the sequence databases. However, the method does not include a function to extract frequent patterns together with gaps or wild character symbols. This new method allows the incorporation of gap characters. Moreover, the method allows effective handling of the annotated sequence database that consists of a set of tuples including a sequence together with a set of items. Furthermore, the prototype has been applied to the evaluation of three sets of sequences that include the Zinc Finger, Cytochrome C, and Kringle motifs.

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Author information

Authors and Affiliations

  1. Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima, 731-3194, Japan

    Hajime Kitakami, Tomoki Kanbara, Yasuma Mori & Susumu Kuroki

  2. Center for Genetic Resource Information, National Institute of Genetics, 1111 Yata, Mishima-Shi, Shizuoka-Ken, 411, Japan

    Yukiko Yamazaki

Authors
  1. Hajime Kitakami
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  2. Tomoki Kanbara
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  3. Yasuma Mori
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  4. Susumu Kuroki
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  5. Yukiko Yamazaki
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Editor information

Editors and Affiliations

  1. School of Information Science and Technology Department of Information and Communication Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan

    Mitsuru Ishizuka

  2. School of Information Technology Knowledge Representation and Reasoning Unit (KRRU) Faculty of Engineering and Information Technology, Griffith University, PMB 50 Gold Coast Mail Centre, Queensland, 9726, Australia

    Abdul Sattar

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© 2002 Springer-Verlag Berlin Heidelberg

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Kitakami, H., Kanbara, T., Mori, Y., Kuroki, S., Yamazaki, Y. (2002). Modified PrefixSpan Method for Motif Discovery in Sequence Databases. In: Ishizuka, M., Sattar, A. (eds) PRICAI 2002: Trends in Artificial Intelligence. PRICAI 2002. Lecture Notes in Computer Science(), vol 2417. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45683-X_52

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  • DOI: https://doi.org/10.1007/3-540-45683-X_52

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44038-3

  • Online ISBN: 978-3-540-45683-4

  • eBook Packages: Springer Book Archive

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