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Protein Motif Prediction by Grammatical Inference

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Grammatical Inference: Algorithms and Applications (ICGI 2006)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4201))

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Abstract

The rapid growth of protein sequence databases is exceeding the capacity of biochemically and structurally characterizing new proteins. Therefore, it is very important the development of tools to locate, within protein sequences, those subsequences with an associated function or specific feature. In our work, we propose a method to predict one of those functional motifs (coiled coil), related with protein interaction. Our approach uses even linear languages inference to obtain a transductor which will be used to label unknown sequences. The experiments carried out show that our method outperforms the results of previous approaches.

Work supported by the CICYT TIC2000-1153 and the Generalitat Valenciana GV06/068.

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Author information

Authors and Affiliations

  1. Departamento de Sistemas Informáticos y Computación., Universidad Politécnica de Valencia., Camino de Vera s/n, 46071, Valencia, SPAIN

    Piedachu Peris, Damián López, Marcelino Campos & José M. Sempere

Authors
  1. Piedachu Peris
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  2. Damián López
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  3. Marcelino Campos
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  4. José M. Sempere
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Editor information

Editors and Affiliations

  1. Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan

    Yasubumi Sakakibara

  2. Dept. of Computer Science, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, Japan

    Satoshi Kobayashi

  3. Japan Biological Informatics Consortium, 10F TIME24 Building, 2-45 Aomi, Koto-ku, 135-8073, Tokyo, Japan

    Kengo Sato

  4. Department of Information and Communication Engineering, Graduate School of Electro-Communications, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu-shi, 182-8585, Tokyo, Japan

    Tetsuro Nishino

  5. Department of Information and Communication Engineering, Faculty of Electro-Communications, The University of Electro-Communications, Chofugaoka 1–5–1, Chofu, 182-8585, Tokyo, Japan

    Etsuji Tomita

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Peris, P., López, D., Campos, M., Sempere, J.M. (2006). Protein Motif Prediction by Grammatical Inference. In: Sakakibara, Y., Kobayashi, S., Sato, K., Nishino, T., Tomita, E. (eds) Grammatical Inference: Algorithms and Applications. ICGI 2006. Lecture Notes in Computer Science(), vol 4201. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11872436_15

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  • DOI: https://doi.org/10.1007/11872436_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-45264-5

  • Online ISBN: 978-3-540-45265-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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