Parallel syntenic alignment on GPUs

Authors:
Junjie Li;Sanjay Ranka;Sartaj Sahni
Affiliations:
University of Florida, Gainesville;University of Florida, Gainesville;University of Florida, Gainesville
Venue:
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2012

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Abstract

We develop novel single-GPU parallel algorithms for syntenic alignment using CUDA. Our algorithms can be used to determine the optimal alignment score as well as the actual optimal alignment for a single pair of sequences. Experimental results show that our best GPU alignment algorithm achieves a speedup of approximately 28 over the sequential algorithm.