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Combining and Comparing Cluster Methods in a Receptor Database

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Advances in Intelligent Data Analysis V (IDA 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2810))

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Abstract

Biological data such as DNA and protein sequences can be analyzed using a variety of methods. This paper combines phylogenetic trees, experience-based classification and self-organizing maps for cluster analysis of G protein-coupled receptors (GPCRs), a class of pharmacologically relevant transmembrane proteins with specific characteristics. This combination allows to gain additional insights.

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References

  1. Graul, R.C., Sadée, W.: Evolutionary relationships among G protein-coupled receptors using a clustered database approach. AAPS Pharmacological Sciences 3(2), E12 (2001)

    Google Scholar 

  2. Karchin, R., Karplus, K., Haussler, D.: Classifying G protein-coupled receptors with support vector machines. Bioinformatics 18(1), 147–159 (2002)

    Article  Google Scholar 

  3. Altschul, S.F., Gish, W., Miller, W., Meyers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. Journal of Molecular Biology 215(3), 403–410 (1990)

    Google Scholar 

  4. Vingron, M., Waterman, M.S.: Sequence alignment and penalty choice. review of concepts, case studies and implications. Journal of Molecular Biology 235(1), 1–12 (1994)

    Article  Google Scholar 

  5. Waterman, M.S.: Parametric and ensemble sequence alignment algorithms. Bulletin of Mathematical Biology 56(4), 743–767 (1994)

    MATH  Google Scholar 

  6. Ferrán, E.A., Ferrara, P.: Clustering proteins into families using artificial neural networks. Computer Applications in Biosciences (CABIOS) 8(1), 39–44 (1992)

    Google Scholar 

  7. Lazović, J.: Selection of amino acid parameters for fourier transform-based analysis of proteins. Computer Applications in Biosciences (CABIOS) 12(6), 553–562 (1996)

    Google Scholar 

  8. Horn, F., Bettler, E., Oliveira, L., Campagne, F., Cohen, F.E., Vriend, G.: GPCRDB information system for G protein-coupled receptors. Nucleic Acids Research 31(1), 294–297 (2003)

    Article  Google Scholar 

  9. Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28(1), 45–48 (2000)

    Article  Google Scholar 

  10. Vriend, G.: WHAT IF: a molecular modeling and drug design program. Journal of Molecular Graphics 8, 52–56 (1990)

    Article  Google Scholar 

  11. Bryant, D.: Optimal agreement supertrees. In: Gascuel, O., Sagot, M.-F. (eds.) JOBIM 2000. LNCS, vol. 2066, pp. 24–31. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  12. Kohonen, T., Hynninen, J., Kangas, J., Laaksonen, J.: SOM PAK: the selforganizing map program package, 2nd edn (1995)

    Google Scholar 

  13. Hanke, J., Reich, J.G.: Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures. Computer Applications in Biosciences (CABIOS) 12(6), 447–454 (1996)

    Google Scholar 

  14. Somervuo, P., Kohonen, T.: Clustering and visualization of large protein sequence databases by means of an extension of the self-organizing map. In: Morishita, S., Arikawa, S. (eds.) DS 2000. LNCS (LNAI), vol. 1967, pp. 76–85. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  15. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., Gibson, T.J.: Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences 23, 403–405 (1998)

    Article  Google Scholar 

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© 2003 Springer-Verlag Berlin Heidelberg

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Samsonova, E.V., Bäck, T., Beukers, M.W., Ijzerman, A.P., Kok, J.N. (2003). Combining and Comparing Cluster Methods in a Receptor Database. In: R. Berthold, M., Lenz, HJ., Bradley, E., Kruse, R., Borgelt, C. (eds) Advances in Intelligent Data Analysis V. IDA 2003. Lecture Notes in Computer Science, vol 2810. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45231-7_32

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  • DOI: https://doi.org/10.1007/978-3-540-45231-7_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40813-0

  • Online ISBN: 978-3-540-45231-7

  • eBook Packages: Springer Book Archive

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