Parallel DC3 Algorithm for Suffix Array Construction on Many-Core Accelerators

Gang Liao, Longfei Ma, Guangming Zang, Lin Tang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

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.
Original languageEnglish (US)
Title of host publication2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
PublisherInstitute of Electrical and Electronics Engineers (IEEE)
Pages1155-1158
Number of pages4
ISBN (Print)9781479980062
DOIs
StatePublished - May 2015

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