Bio-sequence database scanning on a GPU

Weiguo Liu, B. Schmidt, G. Voss, A. Schroder, W. Muller-Wittig
Nanyang Technological University, School of Computer Engineering, Centre for Advanced Media Technology, Singapore 639798
Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International (29 April 2006), 8 pp.


   title={Bio-sequence database scanning on a GPU},

   author={Liu, W. and Schmidt, B. and Voss, G. and Schroder, A. and Muller-Wittig, W.},

   booktitle={Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International},






Download Download (PDF)   View View   Source Source   



Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic programming algorithms exist for this problem, however current solutions still require significant scan times. These scan time requirements are likely to become even more severe due to the rapid growth in the size of these databases. In this paper, we present a new approach to bio-sequence database scanning using computer graphics hardware to gain high performance at low cost. To derive an efficient mapping onto this type of architecture, we have reformulated the Smith-Waterman dynamic programming algorithm in terms of computer graphics primitives. Our OpenGL implementation achieves a speedup of approximately sixteen on a high-end graphics card over available straightforward and optimized CPU Smith-Waterman implementations
No votes yet.
Please wait...

* * *

* * *

HGPU group © 2010-2024 hgpu.org

All rights belong to the respective authors

Contact us: