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Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

Maria Charalambous, Pedro Trancoso, Alexandros Stamatakis
Department of Computer Science, University of Cyprus, 75 Kallipoleos Ave., P.O.Box 20537, 1678 Nicosia, Cyprus
In Advances in Informatics, Vol. 3746 (2005), pp. 415-425.

@article{charalambous2005initial,

   title={Initial experiences porting a bioinformatics application to a graphics processor},

   author={Charalambous, M. and Trancoso, P. and Stamatakis, A.},

   journal={Advances in Informatics},

   pages={415–425},

   year={2005},

   publisher={Springer}

}

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Bioinformatics applications are one of the most relevant and compute-demanding applications today. While normally these applications are executed on clusters or dedicated parallel systems, in this work we explore the use of an alternative architecture. We focus on exploiting the compute-intensive characteristics offered by the graphics processors (GPU) in order to accelerate a bioinformatics application. The GPU is a good match for these applications as it is an inexpensive, high-performance SIMD architecture.
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