Limitations of Current Multicore Architectures for Bioinformatics Applications – A Case Study on Cell BE

The fast growth of biological databases has attracted the attention of computer scientists calling for greater efforts to improve computational performance. From a computer architecture point of view, we intend to investigate how bioinformatics applications can benefit from future multicore processors. Here we present a preliminary study of the Cell BE limitations when executing a representative bioinformatics application performing multiple sequence alignment (i.e. ClustalW). The inherent large parallelism of the core algorithm used makes it ideal for architectures supporting multiple dimensions of parallelism. However, in the case of Cell BE we identified several architectural limitations that need a careful study.