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Exploiting parallel features of modern computer architectures in bioinformatics: applications to genetics, structure comparison and large graph analysis

Guillaume Chapuis
IRISA – Institut de Recherche en Informatique et Systemes Aleatoires
tel-01012222, (25 June 2014)

@phdthesis{guinand2014exploiting,

   title={Exploiting parallel features of modern computer architectures in bioinformatics},

   author={Guinand, Fr{‘e}d{‘e}ric},

   year={2014},

   school={‘E}COLE NORMALE SUP{‘E}RIEURE DE CACHAN}

}

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The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications in genetics with a GPU parallel tool for QTL detection, in protein structure comparison with a multicore parallel tool for finding similar regions between proteins, and large graph analysis with a multi-GPU parallel implementation for a novel algorithm for the All-Pairs Shortest Path problem.
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