TY - GEN
T1 - Parallel DC3 Algorithm for Suffix Array Construction on Many-Core Accelerators
AU - Liao, Gang
AU - Ma, Longfei
AU - Zang, Guangming
AU - Tang, Lin
N1 - KAUST Repository Item: Exported on 2020-10-01
PY - 2015/5
Y1 - 2015/5
N2 - In bioinformatics applications, suffix arrays are widely used to DNA sequence alignments in the initial exact match phase of heuristic algorithms. With the exponential growth and availability of data, using many-core accelerators, like GPUs, to optimize existing algorithms is very common. We present a new implementation of suffix array on GPU. As a result, suffix array construction on GPU achieves around 10x speedup on standard large data sets, which contain more than 100 million characters. The idea is simple, fast and scalable that can be easily scale to multi-core processors and even heterogeneous architectures. © 2015 IEEE.
AB - In bioinformatics applications, suffix arrays are widely used to DNA sequence alignments in the initial exact match phase of heuristic algorithms. With the exponential growth and availability of data, using many-core accelerators, like GPUs, to optimize existing algorithms is very common. We present a new implementation of suffix array on GPU. As a result, suffix array construction on GPU achieves around 10x speedup on standard large data sets, which contain more than 100 million characters. The idea is simple, fast and scalable that can be easily scale to multi-core processors and even heterogeneous architectures. © 2015 IEEE.
UR - http://hdl.handle.net/10754/594134
UR - http://ieeexplore.ieee.org/document/7152610/
UR - http://www.scopus.com/inward/record.url?scp=84941243588&partnerID=8YFLogxK
U2 - 10.1109/ccgrid.2015.56
DO - 10.1109/ccgrid.2015.56
M3 - Conference contribution
SN - 9781479980062
SP - 1155
EP - 1158
BT - 2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
PB - Institute of Electrical and Electronics Engineers (IEEE)
ER -