Traitement parallèle des comparaisons intensives de séquences génomiques

van Hoa Nguyen 1
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : The sequence comparison process is one of the main bioinformatics task. The new sequencing technologies lead to a fast increasing of genomic data and strengthen the need of fast and efficient tools to perform this task. In this thesis, a new algorithm for intensive sequence comparison is proposed. It has been specifically designed to exploit all forms of parallelism of today microprocessors (SIMD instructions, multi-core architecture). This algorithm is also well suited for hardware accelerators such as FPGA or GPU boards. The algorithm has been implemented into the PLAST software (Parallel Local Alignment Search Tool). Different versions are available according to the data to process (protein and/or DNA). A MPI version has also been developed. According to the nature of the data and the type of technologies, speedup from 3 to 20 has been measured compared with the reference software, BLAST, with the same level of quality.
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Submitted on : Tuesday, November 24, 2009 - 5:58:57 PM
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  • HAL Id : tel-00435792, version 1

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van Hoa Nguyen. Traitement parallèle des comparaisons intensives de séquences génomiques. Informatique [cs]. Université Rennes 1, 2009. Français. ⟨tel-00435792⟩

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