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Grid Computing pp 277-291 | Cite as

State-of-Art with PhyloGrid: Grid Computing Phylogenetic Studies on the EELA-2 Project Infrastructure

  • Raul Isea
  • Esther Montes
  • Antonio Juan Rubio-Montero
  • Rafael Mayo
Chapter
Part of the Computer Communications and Networks book series (CCN)

Abstract

PhyloGrid is an application developed in the framework of the EELA-2 project devoted to the calculation of Phylogenies by means of the MrBayes software, that is, Bayesian statistics. To the moment, it has been used to perform studies on the Human Immunodeficiency Virus (HIV), the Human Papillomavirus (HPV), and the DENgue Virus (DENV). PhyloGrid aims to offer an easy interface for the bioinformatics community, which abstracts the final user from the ICT (Information and Communications Technology) underneath, so only the definition of the parameters for doing the Bayesian calculation should be set, including the model of evolution as well as a multiple alignment of the sequences previously to the final result. This chapter provides a description of the application and some new results related to the aforementioned diseases is also shown.

Keywords

Human Immunodeficiency Virus Posterior Probability Markov Chain Monte Carlo Dengue Virus Markov Chain Monte Carlo Sampler 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

Authors thank in particular the support provided by the EELA-2 Project (E-science grid facility for Europe and Latin America, http://www.eu-eela.org), Grant Agreement No. 223797 of the EU Seventh Research Framework Programme-Research Infrastructures.

References

  1. 1.
    Aiken, C., Konner, J., Landau, N.R., Lenburg, M.E., Trono, D.: Nef induces CD4 endocytosis: requirement for a critical dileucine motif in the membrane-proximal CD4 cytoplasmic domain. Cell 76(5), 853–864 (1994)CrossRefGoogle Scholar
  2. 2.
    Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W.: GenBank. Nucleic Acids Res. 38(suppl1), D46–D51 (2010)CrossRefGoogle Scholar
  3. 3.
    Bergsten, J.: A review of long-branch attraction. Cladistics 21(2), 163–193 (2005)CrossRefGoogle Scholar
  4. 4.
    Cadotte, M.W., Cardinale, B.J., Oakley, T.H.: Evolutionary history and the effect of biodiversity on plant productivity. PNAS 105(44), 17012–17017 (2008)CrossRefGoogle Scholar
  5. 5.
    Clamp, M., Cuff, J., Searle, S.M., Barton, G.J.: The Jalview Java Alignment Editor. Bioinformatics 20(3), 426–427 (2004)CrossRefGoogle Scholar
  6. 6.
    Cohen, E., Dehni, G., Sodroski, J.G., Haseltine, W.A.: Human immunodeficiency virus vpr product is a virion-associated regulatory protein. J. Virol. 64(6), 3097–3099 (1990)Google Scholar
  7. 7.
    Cullen, B.R.: HIV-1 Nef protein: an invitation to a kill. Nat. Med. 5(9), 985–986 (1999)CrossRefGoogle Scholar
  8. 8.
    García, J.V., Miller, A.D.: Serine phosphorylation-independent downregulation of cell-surface CD4 by nef. Nature 350, 508–511 (1991)CrossRefGoogle Scholar
  9. 9.
    Hall, B.G., Salipante, S.J.: Measures of clade confidence do not correlate with accuracy of phylogenetic trees. PLoS Comput. Biol. 3(3), e51 (2007)CrossRefGoogle Scholar
  10. 10.
    Huedo, E., Montero, R.S., Llorente, I.M.: The GridWay framework for adaptive scheduling and execution on grids. J. Scalable Comput. Pract. Exp. 6(3), 1–8 (2005)Google Scholar
  11. 11.
    Huelsenbeck, J.P., et al.: Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51, 673–688 (2002)CrossRefGoogle Scholar
  12. 12.
    Isea, R., Montes, E., Rubio-Montero, A.J., Mayo, R.: Computational challenges on grid computing for workflows applied to phylogeny. LNCS 5518, 1130–1138 (2009)Google Scholar
  13. 13.
    Isea, R., Montes, E., Rubio-Montero, A.J., Mayo, R.: Challenges and characterization of a Biological system on Grid by means of the PhyloGrid application. In: Proceedings of the 1st EELA-2 Conference, Bogota, pp. 139–146 (2009b)Google Scholar
  14. 14.
    Isea, R., Montes, E., Rubio-Montero, A.J., Rosales, J.D., Rodríguez-Pascual, M.A., Mayo, R.: Characterization of antigenetic serotypes from the dengue virus in Venezuela by means of Grid Computing. In: Solomonides, T., Blanquer, I., Breton, V., Glatard, T., Legré, Y. (eds.) Studies in Health Technology and Informatics 159:234–238 (2010)Google Scholar
  15. 15.
    Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, H.B., Wolinsky, S., Bhattacharya, T.: Timing the ancestor of the HIV-1 pandemic strains. Science 288(5472), 1789–1796 (2000)CrossRefGoogle Scholar
  16. 16.
    Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., Higgins, D.G.: CLUSTAL W and CLUSTALX version 2.0. Bioinformatics 23(21), 2947–2948 (2007)CrossRefGoogle Scholar
  17. 17.
    Lowy, D.R., Schiller, J.T.: Prophylactic human papillomavirus vaccines. J. Clin. Investig. 116(5), 1167–1173 (2006)CrossRefGoogle Scholar
  18. 18.
    McAuliffe, J.D., Pachter, L., Jordan, M.I.: Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics 20(12), 1850–1860 (2004)CrossRefGoogle Scholar
  19. 19.
    Montes, E., Isea, R., Mayo, R.: PhyloGrid: A development for a workflow in Phylogeny. In: Silva, F. (ed.) Second Iberian Grid Infrastructure Conference Proceedings, pp. 378–387. Netbiblo, Cristina (2008)Google Scholar
  20. 20.
    Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L., Swofford, D.L.: AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24(4), 581–583 (2004)CrossRefGoogle Scholar
  21. 21.
    Oinn, T., et al.: Taverna: lessons in creating a workflow environment for the life sciences. Concurrency Comput. Pract. Exp. 18(10), 1067–1100 (2005)CrossRefGoogle Scholar
  22. 22.
    Page, R.: Tree View: An application to display phylogenetic trees on personal computers. Bioinformatics 12, 357–358 (1996)CrossRefGoogle Scholar
  23. 23.
    Pennisi, E.: Revising HIV’s History. ScienceNOW. Retrieved from http://sciencenow.sciencemag.org/cgi/content/full/2008/625/1 (2008)
  24. 24.
    Pérez, J., Castañeda-García, A., Jenke-Kodama, H., Müller, R., Muñoz-Dorado, J.: Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome. PNAS 105(41), 15950–15955 (2008)CrossRefGoogle Scholar
  25. 25.
    Posada, D.: jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256 (2008)CrossRefGoogle Scholar
  26. 26.
    Rannala, B., Yang, Z.: Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43(3), 304–311 (1996)CrossRefGoogle Scholar
  27. 27.
    Ronquist, F., Huelsenbeck, J.P.: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12), 1572–1574 (2003)CrossRefGoogle Scholar
  28. 28.
    Sun, J., Xu, J., Liu, Z., Liu, Q., Zhao, A., Shi, T., Li, Y.: Refined phylogenetic profiles method for predicting protein–protein interactions. Bioinformatics 21(16), 3409–3415 (2005)CrossRefGoogle Scholar
  29. 29.
    Thomas, M., Gilbert, P., Rambaut, A., Wlasiuk, G., Spira, J.T., Pitchenik, E.A., Worobey, M.: The emergence of HIV/AIDS in the Americas and beyond. Proc. Natl. Acad. Sci. U.S.A 104, 18566–18570 (2007)CrossRefGoogle Scholar
  30. 30.
    Woese, C.R.: The universal ancestor. Proc. Natl. Acad. Sci U.S.A 95, 6854–6859 (1998)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London Limited 2011

Authors and Affiliations

  • Raul Isea
    • 1
  • Esther Montes
    • 2
  • Antonio Juan Rubio-Montero
    • 2
  • Rafael Mayo
    • 2
  1. 1.Fundación IDEACaracasVenezuela
  2. 2.Centro de Investigaciones Energeticas Medioambientales y Tecnologicas (CIEMAT)MadridSpain

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