Preliminary analysis of the cell BE processor limitations for sequence alignment applications
Document typeConference report
Rights accessRestricted access - publisher's policy
The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multi-core processors. In this paper we present a preliminary study of the Cell BE processor limitations when executing two representative sequence alignment applications (Ssearch and ClustalW). The inherent large parallelism of the targeted algorithms makes them ideal for architectures supporting multiple dimensions of parallelism (TLP and DLP). However, in the case of Cell BE we identified several architectural limitations that need a careful study and quantification.
CitationIsaza, S.; Sánchez, F.; Gaydadjiev, G.; Ramírez, A.; Valero, M. Preliminary analysis of the cell BE processor limitations for sequence alignment applications. A: International Workshop on Systems, Architectures, Modeling and Simulation. "Embedded Computer Systems: Architectures, Modeling, and Simulation: 8th International Workshop, SAMOS 2008: Samos, Greece, July 21-24, 2008: proceedings". Springer, 2008, p. 53-64.
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