Long DNA sequence comparison on multicore architectures

Authors:
Friman Sánchez;Felipe Cabarcas;Alex Ramirez;Mateo Valero
Affiliations:
Technical University of Catalonia, Barcelona, Spain;Barcelona Supercomputing Center, BSC, Spain and Universidad de Antioquia, Colombia;Technical University of Catalonia, Barcelona, Spain and Barcelona Supercomputing Center, BSC, Spain;Technical University of Catalonia, Barcelona, Spain and Barcelona Supercomputing Center, BSC, Spain
Venue:
Euro-Par'10 Proceedings of the 16th international Euro-Par conference on Parallel processing: Part II
Year:
2010

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Abstract

Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially when very long sequences are compared. The Smith-Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. The inherent large parallelism of the algorithm makes it ideal for architectures supporting multiple dimensions of parallelism (TLP, DLP and ILP). In this work, we show how long sequences comparison takes advantage of current and future multicore architectures. We analyze two different SW implementations on the CellBE and use simulation tools to study the performance scalability in a multicore architecture. We study the memory organization that delivers the maximum bandwidth with the minimum cost. Our results show that a heterogeneous architecture is an valid alternative to execute challenging bioinformatic workloads.