采用BWT的多核并行的子串匹配算法

针对P-BWT精确匹配算法存在只支持短串查询并且只能工作在单处理器上的问题,提出了一个多核并行的支持任意查询长度的精确查询算法.改进了P-BWT索引上的查询过程,当一个查询串跨越了多个数据分片时,首先在其匹配的最后一个分片上查询,然后依次在前面分片上进行验证.进一步提出了一个多核并行查询算法来减少搜索和验证过程的迭代次数.实验结果表明,所述算法可以高效并行地完成子串匹配任务....

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Bibliographic Details
Published in东北大学学报（自然科学版） Vol. 37; no. 5; pp. 624 - 628
Main Author 王佳英 王斌 李晓华 杨晓春
Format Journal Article
LanguageChinese
Published 东北大学计算机科学与工程学院,辽宁 沈阳,110819 2016
Subjects
BWT
全文索引
多核
并行
精确匹配
multi-core
多核
full text index
parallel
精确匹配
exact matching
BWT (Burrows-Wheeler transform)
并行
BWT
全文索引
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Summary:针对P-BWT精确匹配算法存在只支持短串查询并且只能工作在单处理器上的问题,提出了一个多核并行的支持任意查询长度的精确查询算法.改进了P-BWT索引上的查询过程,当一个查询串跨越了多个数据分片时,首先在其匹配的最后一个分片上查询,然后依次在前面分片上进行验证.进一步提出了一个多核并行查询算法来减少搜索和验证过程的迭代次数.实验结果表明,所述算法可以高效并行地完成子串匹配任务.
Bibliography:In order to solve the problem that P-BWT （Burrows-Wheeler transform） could only support short queries, and work on a uniprocessor, a multi-core parallel exact matching algorithm was proposed which any query length could be supposed. Firstly, the search process on P-BWT index was modified. When a query spans multiple data fragments, it first searches on the last segment, then verifies on the other segments. Further, a parallel algorithm was proposed to reduce the iterations in the search and verify process. Finally, the experimental study show that using the proposed algorithm, the substring matching task could be accomplished efficiently in parallel manner.
BWT （ Burrows-Wheeler transform） ; full text index; exact matching; parallel;multi-core
21-1344/T
WANG Jia-ying, WANG Bin, LI Xiao-hua, YANG Xiao-chun （ School of Computer Science ＆ Engineering, Northeastern University, Shenyang 110819, China）
ISSN:1005-3026
DOI:10.3969/j.issn.1005-3026.2016.05.004