Abstract
New analytical methodologies, like the so-called “next-generation sequencing” (NGS), allow the sequencing of full genomes with high speed and reduced price. Yet, such technologies generate huge amounts of data that demand large raw computational power. Many-core technologies can be exploited to overcome the involved bioinformatics bottleneck. Indeed, such hardware is currently in active development. We have developed parallel bioinformatics algorithms for many-core microprocessors containing 64 cores each. Thus, the MC64 web platform allows executing high-performance alignments (Needleman-Wunsch, Smith-Waterman and ClustalW) of long sequences. The MC64 platform can be accessed via web browsers, allowing easy resource integration into third-party tools. Furthermore, the results obtained from the MC64 include time-performance statistics that can be compared with other platforms.
This is a preview of subscription content, log in via an institution to check access.
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
Howard, J., Dighe, S., Hoskote, Y., Vangal, S., Finan, D., Ruhl, G., Jenkins, D., Wilson, H., Borkar, N., Schrom, G., et al.: A 48-Core IA-32 Message-Passing Processor with DVFS in 45nm CMOS. In: International Solid-State Circuits Conference, 2010 ISSCC 2010 Digest of Technical Papers IEEE International, pp. 19–21 (2010)
Skaugen, K.: Petascale to Exascale. In: International Supercomputing Conference, Hamburg, Germany (2010)
Bell, S., Edwards, B., Amann, J., Conlin, R., Joyce, K., Leung, V., MacKay, J., Reif, M., Bao, L., Brown, J., et al.: TILE64 - Processor: A 64-Core SoC with Mesh Interconnect. In: Solid-State Circuits Conference, 2008 ISSCC 2008 Digest of Technical Papers IEEE International, pp. 588–598 (2008)
Mike Tate, R.J., Behrooz A.: NetLogic Microsystems, Inc. Q3 2010 Earnings Conference Call Transcript. In: Thomson StreetEvents (2010)
Shah, M., Barreh, J., Brooks, J., Golla, R., Grohoski, G., Gura, N., Hetherington, R., Jordan, P., Luttrell, M., Olson, C., et al.: UltraSPARC T2: A highly-treaded, power-efficient. In: SPARC SOC Asian Solid-State Circuits Conference (ASSCC 2007), pp. 22–25 (2007)
Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48(3), 443–453 (1970)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195–197 (1981)
Gálvez, S., Díaz, D., Hernández, P., Esteban, F.J., Caballero, J.A., Dorado, G.: Next-Generation Bioinformatics: Using Many-Core Processor Architecture to Develop a Web Service for Sequence Alignment. Bioinformatics 26(5), 683–686 (2010)
Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994)
Driga, A., Lu, P., Schaeffer, J., Szafron, D., Charter, K., Parsons, I.: FastLSA: A Fast, Linear-Space, Parallel and Sequential Algorithm for Sequence Alignment. Algorithmica 45(3), 337–375 (2006)
Hirschberg, D.S.: A linear space algorithm for computing maximal common subsequences. Commun. ACM 18(6), 341–343 (1975)
Li, K.-B.: ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19(12), 1585–1586 (2003)
Díaz, D., Gálvez, S., Falgueras, J., Caballero, J.A., Hernández, P., Claros, G., Dorado, G.: Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework. In: Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, pp. 1084–1091. Springer, Salamanca (2009)
Altschul, S., Gish, W., Miller, W., Myers, E.-M., Lipman, D.: Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)
Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., Barton, G.J.: Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9), 1189–1191 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Esteban, F.J., Díaz, D., Hernández, P., Caballero, J.A., Dorado, G., Gálvez, S. (2011). MC64: A Web Platform to Test Bioinformatics Algorithms in a Many-Core Architecture. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A. (eds) 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Advances in Intelligent and Soft Computing, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19914-1_2
Download citation
DOI: https://doi.org/10.1007/978-3-642-19914-1_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-19913-4
Online ISBN: 978-3-642-19914-1
eBook Packages: EngineeringEngineering (R0)