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Title:
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Scalability analysis of progressive alignment in a multicore
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Author:
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Isaza, Sebastian; Sánchez Castaño, Friman; Gaydadjiev, Georgi; Ramírez Bellido, Alejandro; Valero Cortés, Mateo
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Other authors:
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Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors; Universitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions |
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Abstract:
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Sequence alignment is a fundamental instrument in Bioinformatics. In recent years, numerous proposals have been
addressing the problem of accelerating this class of applications. This, due to the rapid growth of sequence databases in
combination with the high computational demands imposed by the algorithms. In this paper we focus on the analysis of the
progressive alignment in ClustalW, a widely used program for performing multiple sequence alignment. We have parallelized
ClustalW for the Cell processor architecture and have carefully analyzed the scalability of its different phases with both the
number of cores used and the input size. Experimental results show that computing profile scores scales well up to 16 SPE cores. With the increase of the input size, profiles initialization in the PPE core becomes the predominant bottleneck. |
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Abstract:
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Peer Reviewed |
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Subject(s):
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-Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
-Àrees temàtiques de la UPC::Informàtica::Sistemes d'informació::Bases de dades
-Bioinformatics
-Database Management Systems
-Software architecture
-Bioinformàtica
-Programari -- Arquitectura
-Bases de dades -- Gestió |
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Rights:
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Document type:
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Article - Published version
Conference Object |
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Published by:
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IEEE Press. Institute of Electrical and Electronics Engineers
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