IT Revolutions. Third International ICST Conference, Córdoba, Spain, March 23-25, 2011, Revised Selected Papers

Research Article

Many-Core Processor Bioinformatics and Next-Generation Sequencing

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  • @INPROCEEDINGS{10.1007/978-3-642-32304-1_15,
        author={Francisco Esteban and David D\^{\i}az and Pilar Hern\^{a}ndez and Juan Caballero and Gabriel Dorado and Sergio G\^{a}lvez},
        title={Many-Core Processor Bioinformatics and Next-Generation Sequencing},
        proceedings={IT Revolutions. Third International ICST Conference, C\^{o}rdoba, Spain, March 23-25, 2011, Revised Selected Papers},
        proceedings_a={IT REVOLUTIONS},
        year={2012},
        month={10},
        keywords={Parallel Computing Grid and Cloud Computing Biotechnology Agrifood and Agribusiness},
        doi={10.1007/978-3-642-32304-1_15}
    }
    
  • Francisco Esteban
    David Díaz
    Pilar Hernández
    Juan Caballero
    Gabriel Dorado
    Sergio Gálvez
    Year: 2012
    Many-Core Processor Bioinformatics and Next-Generation Sequencing
    IT REVOLUTIONS
    Springer
    DOI: 10.1007/978-3-642-32304-1_15
Francisco Esteban1,*, David Díaz2,*, Pilar Hernández3,*, Juan Caballero1,*, Gabriel Dorado1,*, Sergio Gálvez2,*
  • 1: Universidad de Córdoba
  • 2: Universidad de Málaga
  • 3: Instituto de Agricultura Sostenible (IAS – CSIC)
*Contact email: fjesteban@uco.es, david.diaz@lcc.uma.es, phernandez@ias.csic.es, ma1camoj@uco.es, bb1dopeg@uco.es, galvez@lcc.uma.es

Abstract

The new massive DNA sequencing methods demand both computer hardware and bioinformatics software capable of handling huge amounts of data. This paper shows how the many-core processors (in which each core can execute a whole operating system) can be exploited to address problems which previously required expensive supercomputers. Thus, the Needleman-Wunsch/Smith-Waterman pairwise alignments will be described using long DNA sequences (>100 kb), including the implications for progressive multiple alignments. Likewise, assembling algorithms used to generate contigs on sequencing projects (therefore, using short sequences) and the future in peptide (protein) folding computing methods will be also described. Our study also integrates the last trends in many-core processors and their applications in the field of bioinformatics.