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Many-Core Processor Bioinformatics and Next-Generation Sequencing

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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.

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Author information

Authors and Affiliations

  1. Servicio de Informática, Universidad de Córdoba, Campus Rabanales, 14071, Córdoba, Spain

    Francisco J. Esteban

  2. Dep. Lenguajes y Ciencias de la Computación, Universidad de Málaga, Boulevard Louis Pasteur 17, 29071, Málaga, Spain

    David Díaz & Sergio Gálvez

  3. Instituto de Agricultura Sostenible (IAS – CSIC), Alameda del Obispo s/n, 14080, Córdoba, Spain

    Pilar Hernández

  4. Dep. Estadística, Universidad de Córdoba, Campus Rabanales, 14071, Córdoba, Spain

    Juan Antonio Caballero

  5. Dep. Bioquímica y Biología Molecular, Universidad de Córdoba, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), 14071, Córdoba, Spain

    Gabriel Dorado

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  1. Francisco J. Esteban
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  2. David Díaz
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  3. Pilar Hernández
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  4. Juan Antonio Caballero
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  5. Gabriel Dorado
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  6. Sergio Gálvez
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Editor information

Editors and Affiliations

  1. Universidad de Córdoba, Spain

    Matías Liñán Reyes , José M. Flores Arias , Francisco J. Bellido Outeiriño  & Antonio Moreno-Munñoz , ,  & 

  2. University of Cádiz, Spain

    Juan J. González de la Rosa

  3. Fachhochschule Hagenberg, Austria

    Josef Langer

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© 2012 ICST Institute for Computer Science, Social Informatics and Telecommunications Engineering

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Esteban, F.J., Díaz, D., Hernández, P., Caballero, J.A., Dorado, G., Gálvez, S. (2012). Many-Core Processor Bioinformatics and Next-Generation Sequencing. In: Liñán Reyes, M., Flores Arias, J.M., González de la Rosa, J.J., Langer, J., Bellido Outeiriño, F.J., Moreno-Munñoz, A. (eds) IT Revolutions. IT Revolutions 2011. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 82. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32304-1_15

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  • DOI: https://doi.org/10.1007/978-3-642-32304-1_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-32303-4

  • Online ISBN: 978-3-642-32304-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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