TY - GEN
T1 - Scalability analysis of progressive alignment on a multicore
AU - Isaza, Sebastian
AU - Sanchez, Friman
AU - Gaydadjiev, Georgi
AU - Ramirez, Alex
AU - Valero, Mateo
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=77952692885&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77952692885&partnerID=8YFLogxK
U2 - 10.1109/CISIS.2010.149
DO - 10.1109/CISIS.2010.149
M3 - Conference contribution
AN - SCOPUS:77952692885
SN - 9780769539676
T3 - CISIS 2010 - The 4th International Conference on Complex, Intelligent and Software Intensive Systems
SP - 889
EP - 894
BT - 4th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS-2010
T2 - 4th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS-2010
Y2 - 15 February 2010 through 18 February 2010
ER -