Combining and Comparing Cluster Methods in a Receptor Database

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.

[1]  J. Lazovic,et al.  Selection of amino acid parameters for Fourier transform-based analysis of proteins , 1996, Comput. Appl. Biosci..

[2]  J. Thompson,et al.  Multiple sequence alignment with Clustal X. , 1998, Trends in biochemical sciences.

[3]  David Haussler,et al.  Classifying G-protein coupled receptors with support vector machines , 2002, Bioinform..

[4]  Jens G. Reich,et al.  Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures , 1996, Comput. Appl. Biosci..

[5]  M S Waterman.  Parametric and ensemble sequence alignment algorithms. , 1994, Bulletin of mathematical biology.

[6]  Edgardo A. Ferrán,et al.  Clustering proteins into families using artificial neural networks [published erratum appears in Comput Appl Biosci 1992 Jun;8(3): 305] , 1992, Comput. Appl. Biosci..

[7]  M S Waterman,et al.  Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.

[8]  Jorma Laaksonen,et al.  SOM_PAK: The Self-Organizing Map Program Package , 1996 .

[9]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[10]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[11]  Panu Somervuo,et al.  Clustering and Visualization of Large Protein Sequence Databases by Means of an Extension on the Self-Organizing Map , 2000, Discovery Science.

[12]  Gert Vriend,et al.  GPCRDB information system for G protein-coupled receptors , 2003, Nucleic Acids Res..

[13]  David Bryant.  Optimal Agreement Supertrees , 2000, JOBIM.

[14]  Jill P. Mesirov,et al.  Computational Biology , 2018, Encyclopedia of Parallel Computing.