Abstract
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 efficient 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.
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© 2006 Springer-Verlag Berlin Heidelberg
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Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W. (2006). GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. In: Robert, Y., Parashar, M., Badrinath, R., Prasanna, V.K. (eds) High Performance Computing - HiPC 2006. HiPC 2006. Lecture Notes in Computer Science, vol 4297. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11945918_37
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DOI: https://doi.org/10.1007/11945918_37
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-68039-0
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