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Complementing Kernel-Based Visualization of Protein Sequences with Their Phylogenetic Tree

  • Martha Ivón Cárdenas
  • Alfredo Vellido
  • Iván Olier
  • Xavier Rovira
  • Jesús Giraldo
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7548)

Abstract

The world of pharmacology is becoming increasingly dependent on the advances in the fields of genomics and proteomics. This dependency brings about the challenge of finding robust methods to analyze the complex data they generate. In this brief paper, we focus on the analysis of a specific type of proteins, the G protein-couple receptors, which are the target for over 15% of current drugs. We describe a kernel method of the manifold learning family for the analysis and intuitive visualization of their protein amino acid symbolic sequences. This method is shown to reveal the grouping structure of the sequences in a way that closely resembles the corresponding phylogenetic trees.

Keywords

Kernel GTM Phylogenetic Tree Data Visualization GPCR Protein Sequence 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Martha Ivón Cárdenas
    • 1
  • Alfredo Vellido
    • 1
  • Iván Olier
    • 2
  • Xavier Rovira
    • 3
  • Jesús Giraldo
    • 4
  1. 1.Departament de Llenguatges i Sistemes InformàticsUniversitat Politècnica de CatalunyaBarcelonaSpain
  2. 2.School of Psychological SciencesThe University of ManchesterManchesterUnited Kingdom
  3. 3.Department of Molecular Pharmacology Institute of Functional Genomics (IGF) CNRS UMR5203, INSERM U661University of MontpellierMontpellier cedex 5France
  4. 4.Institut de Neurociències, Unitat de BioestadísticaUniversitat Autònoma de BarcelonaBarcelonaSpain

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