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MC64: A Web Platform to Test Bioinformatics Algorithms in a Many-Core Architecture

  • Francisco José Esteban
  • David Díaz
  • Pilar Hernández
  • Juan Antonio Caballero
  • Gabriel Dorado
  • Sergio Gálvez
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)

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.

Keywords

Pairwise Alignment Bioinformatics Algorithm Dynamic Program Matrix MC64 Algorithm Multiple Alignment Algorithm 
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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Francisco José Esteban
    • 1
  • David Díaz
    • 2
  • Pilar Hernández
    • 3
  • Juan Antonio Caballero
    • 4
  • Gabriel Dorado
    • 5
  • Sergio Gálvez
    • 2
  1. 1.Servicio de InformáticaUniversidad de CórdobaCórdobaSpain
  2. 2.Dep. Lenguajes y CC. de la ComputaciónUniversidad de MálagaMálagaSpain
  3. 3.Instituto de Agricultura Sostenible (IAS-CSIC)CórdobaSpain
  4. 4.Dep. EstadísticaUniversidad de CórdobaCórdobaSpain
  5. 5.Dep. Bioquímica y Biología MolecularUniversidad de CórdobaCórdobaSpain

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