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GPU-ClustalW: Using graphics hardware to accelerate multiple sequence alignment

: Liu, Weiguo; Schmidt, Bertil; Voss, Gerrit; Müller-Wittig, Wolfgang K.


Robert, Y.:
High performance computing - HiPC 2006. 13th international conference 2006 : Bangalore, India, December 18-21, 2006; Proceedings
Berlin: Springer, 2006 (Lecture Notes in Computer Science 4297)
ISBN: 3-540-68039-X
ISBN: 978-3-540-68039-0
International Conference on High Performance Computing (HiPC) <13, 2006, Bangalore>
Fraunhofer IGD ()
computer architecture; graphics hardware; dynamic programming; Graphic Processing Unit (GPU); alignment

Molecular Biologists frequently compute multiple sequence alignments (MSAs) to identify similar regions in protein families. However, aligning hundreds of sequences by popular MSA tools such as ClustalW requires several hours on sequential computers. Due to the rapid growth of biological sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to reduce this runtime using graphics processing units (GPUs). To derive an effient mapping onto this type of architecture, we have reformulated the computationally most expensive part of ClustalW in terms of computer graphics primitives. This results in a high-speed implementation with significant runtime savings on a commodity graphics card.