Abstract
PhyloGrid is a new tool continuously in progress whose aim is two-fold: to reduce the technological divide that a partial scientific community with low computational skills has for accessing new powerful computational platforms such as Grid; and, to develop a user-friendly interface by means of a workflow integrated in a web-portal. MrBayes software has been selected for calculating the evolutionary history of the species which is being integrated into new tools that performs the execution of jobs. Finally, this new application has been tested on the Human Papillomavirus.
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References
Krane, D.E., Raymer, M.L.: Fundamental Concepts of Bioinformatics. Benjamin Cummings, New Jersey (2002)
Michu, E.: A short guide to phylogeny reconstruction. Plant Soil Environ. 53, 442–446 (2007)
Chan, S.Y., et al.: Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy. J. Virol. 69, 3074–3083 (1995)
Pennisi, E.: Revising HIV’s History. ScienceNOW Daily News (June 25, 2008), http://sciencenow.sciencemag.org/cgi/content/full/2008/625/1
Gottschling, M., et al.: Multiple Evolutionary Mechanisms Drive Papillomavirus Diversification. Molecular Biology and Evolution 24, 1242–1258 (2007)
Keane, T.M., Naughton, T.J., Travers, S.A., McInerney, J.O., Mc-Cormack, G.P.: DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21, 969–974 (2005)
Minh, B.Q., Vinh, L.S., Haeseler, A., Schmidt, H.A.: pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics 21, 3794–3796 (2005)
Lowy, D.R., Schiller, J.T.: Prophylactic human papillomavirus vaccines. J. Clin. Invest. 116, 1167–1173 (2006)
Steller, M.A.: Human papillomavirus, it’s genes. and cancer vaccines. Cancer Cell. 3, 7–8 (2003)
Ronquist, F., Huelsenbeck, J.P.: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)
Oinn, T., et al.: Taverna: lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice and Experience 18, 1067–1100 (2006)
Rannala, B., Yang, Z.: Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Molecular Evolution 43, 304–311 (1996)
Huelsenbeck, J.P., Larget, B., Miller, R.E., Ronquist, F.: Potential Applications and Pitfalls of Bayesian Inference of Phylogeny. Syst. Biol. 51, 673–688 (2002)
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, 15950–15955 (2008)
Gridsphere, http://www.gridsphere.org/gridsphere/gridsphere/guest/home/r
Yang, X., Dong, X., Wang, R.A.: Development of standards-based grid portals, Part2: JSR 168 grid portlets, http://epubs.cclrc.ac.uk/bitstream/1434/article07B.pdf
Huedo, E., Montero, R.S., Llorente, I.M.: The GridWay Framework for Adaptive Scheduling and Execution on Grids. Scalable Computing-Practice and Experience 6, 1–8 (2005)
Vázquez, T., Huedo, E., Montero, R.S., Llorente, I.M.: Evaluation of a Utility Computing Model Based on the Federation of Grid Infrastructures. In: Kermarrec, A.-M., Bougé, L., Priol, T. (eds.) Euro-Par 2007. LNCS, vol. 4641, pp. 372–381. Springer, Heidelberg (2007)
Page, R.: Tree View: An application to display phylogenetic trees on personal computers. Bioinformatics 12, 357–358 (1996)
Muñoz, N., Bosch, F.X., Sanjosé, S., Herrero, R., Castellsagué, X., Shah, K.V., Snijders, P.J., Meijer, C.J.: Epidemiologic classification of human papillomavirus types associated with cervical cancer. N. Engl. J. Med. 348, 518–527 (2003)
Matsukura, T., Sugase, M.: Pitfalls in the epidemiologic classification of human papillomavirus types associated with cervical cancer using polymerase chain reaction: driver and passenger. Int. J. Gynecological Cancer 18, 1042–1050 (2008)
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Isea, R., Montes, E., Rubio-Montero, A.J., Mayo, R. (2009). Computational Challenges on Grid Computing for Workflows Applied to Phylogeny. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_171
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DOI: https://doi.org/10.1007/978-3-642-02481-8_171
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