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Scalability analysis of progressive alignment in a multicore
Isaza, Sebastian; Sánchez Castaño, Friman; Gaydadjiev, Georgi; Ramírez Bellido, Alejandro; Valero Cortés, Mateo
Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors; Universitat Politècnica de Catalunya. CAP - Grup de Computació d´Altes Prestacions
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.
Peer Reviewed
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
info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
IEEE Press. Institute of Electrical and Electronics Engineers
         

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