A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

The Viterbi algorithm is the compute-intensive kernel in Hidden Markov Model (HMM) based sequence alignment applications. In this paper, we investigate extending several parallel methods, such as the wave-front and streaming methods for the Smith-Waterman algorithm, to achieve a significant speed-up...

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Bibliographic Details

Published in:	2010 IEEE International Symposium on Parallel and Distributed Processing, Workshops and Phd Forum pp. 1 - 8
Main Authors:	Zhihui Du, Zhaoming Yin, Bader, David A
Format:	Conference Proceeding
Language:	English
Published:	IEEE 01.04.2010
Subjects:	Algorithm design and analysis Biology computing Concurrent computing Decoding GPGPU Graphics Heuristic algorithms hidden Markov model Hidden Markov models Kernel Tiles Viterbi algorithm
ISBN:	9781424465330, 1424465338
Online Access:	Get full text
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