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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 49–58Cite as

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Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns

Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns

  • Masae Hosoda23,
  • Yukie Akune23 &
  • Kiyoko F. Aoki-Kinoshita23 
  • Conference paper
  • 1598 Accesses

  • 6 Citations

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

The purpose of our research is the elucidation of glycan recognition patterns. Glycans are composed of monosaccharides and have complex structures with branches due to the fact that monosaccharides have multiple potential binding positions compared to amino acids. Each monosaccharide can potentially be bound by up to five other monosaccharides, compared to two for any amino acid. Glycans are often bound to proteins and lipids on the cell surface and play important roles in biological processes. Lectins in particular are proteins that recognize and bind to glycans. In general, lectins bind to the terminal monosaccharides of glycans on glycoconjugates. However, it is suggested that some lectins recognize not only terminal monosaccharides, but also internal monosaccharides, possibly influencing the binding affinity. Such analyses are difficult without novel bioinformatics techniques. Thus, in order to better understand the glycan recognition mechanism of such biomolecules, we have implemented a novel algorithm for aligning glycan tree structures, which we provide as a web tool called MCAW (Multiple Carbohydrate Alignment with Weights). From our web tool, we have analyzed several different lectins, and our results could confirm the existence of well-known glycan motifs. Our work can now be used in several other analyses of glycan structures, such as in the development of glycan score matrices as well as in state model determination of probabilistic tree models. Therefore, this work is a fundamental step in glycan pattern analysis to progress glycobiology research.

Keywords

  • glycomics
  • glycans
  • bioinformatics
  • multiple tree alignment algorithm

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Author information

Authors and Affiliations

  1. Dept. of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, Japan, 192-8577

    Masae Hosoda, Yukie Akune & Kiyoko F. Aoki-Kinoshita

Authors
  1. Masae Hosoda
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  2. Yukie Akune
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  3. Kiyoko F. Aoki-Kinoshita
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Hosoda, M., Akune, Y., Aoki-Kinoshita, K.F. (2012). Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_5

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_5

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