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Preliminary analysis of the cell BE processor limitations for sequence alignment applications
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
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.
Peer Reviewed
Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
Bioinformatics -- Data processing
Arquitectura de computadors
Bioinformàtica
info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Springer
         

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