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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Graul, R.C., Sadée, W.: Evolutionary relationships among G protein-coupled receptors using a clustered database approach. AAPS Pharmacological Sciences 3(2), E12 (2001)
Karchin, R., Karplus, K., Haussler, D.: Classifying G protein-coupled receptors with support vector machines. Bioinformatics 18(1), 147–159 (2002)
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)
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)
Waterman, M.S.: Parametric and ensemble sequence alignment algorithms. Bulletin of Mathematical Biology 56(4), 743–767 (1994)
Ferrán, E.A., Ferrara, P.: Clustering proteins into families using artificial neural networks. Computer Applications in Biosciences (CABIOS) 8(1), 39–44 (1992)
Lazović, J.: Selection of amino acid parameters for fourier transform-based analysis of proteins. Computer Applications in Biosciences (CABIOS) 12(6), 553–562 (1996)
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)
Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28(1), 45–48 (2000)
Vriend, G.: WHAT IF: a molecular modeling and drug design program. Journal of Molecular Graphics 8, 52–56 (1990)
Bryant, D.: Optimal agreement supertrees. In: Gascuel, O., Sagot, M.-F. (eds.) JOBIM 2000. LNCS, vol. 2066, pp. 24–31. Springer, Heidelberg (2001)
Kohonen, T., Hynninen, J., Kangas, J., Laaksonen, J.: SOM PAK: the selforganizing map program package, 2nd edn (1995)
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)
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)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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
Download citation
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