Scalability analysis of progressive alignment on a multicore

Sebastian Isaza, Friman Sanchez, Georgi Gaydadjiev, Alex Ramirez, Mateo Valero

Producción científica: Capítulo en Libro/ReporteContribución a la conferencia

4 Citas (Scopus)

Resumen

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.

Idioma originalInglés estadounidense
Título de la publicación alojada4th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS-2010
Páginas889-894
Número de páginas6
DOI
EstadoPublicada - 2010
Publicado de forma externa
Evento4th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS-2010 - Krakow, Polonia
Duración: feb. 15 2010feb. 18 2010

Serie de la publicación

NombreCISIS 2010 - The 4th International Conference on Complex, Intelligent and Software Intensive Systems

Conferencia

Conferencia4th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS-2010
País/TerritorioPolonia
CiudadKrakow
Período2/15/102/18/10

Áreas temáticas de ASJC Scopus

  • Inteligencia artificial
  • Software

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