Journal of Software:2016.27(7):1715-1728

(东北大学 计算机科学与工程学院, 辽宁 沈阳 110819)
Efficient Compressed Genomic Data Oriented Query Approach
WANG Jia-Ying,WANG Bin,YANG Xiao-Chun
(School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China)
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Received:September 25, 2015    Revised:January 12, 2016
> 中文摘要: 随着下一代、第三代等测序技术的快速发展,DNA等生物序列数据快速增长.如何高效地处理这些大数据是目前所面临的一个挑战.研究发现,这些生物序列数据尽管很大,但是不同数据之间具有很高的相似性.因此可以通过保存这些基因串同一个基准序列之间的差异来减少存储的代价.最新的研究发现,可以在这些压缩的数据上直接进行查询,而不需要解压缩.研究的目标是进一步提高索引和查询的可伸缩性,从而满足日益增长的大数据需要.首先在现有方法的基础上,对基准序列进行了压缩存储.基于该压缩数据,提出了一系列优化查询方法以高效地支持任意长度序列的精确和近似查询.在此基础上,进一步对原有方法进行改进,利用并行计算来提高对大数据的查询效率.最后,实验研究展示了所提方法的高效性.
Abstract:With the rapid development of the third and next generation sequencing techniques, genomic sequences such as DNA grow explosively. Processing such big data efficiently is a great challenge. Research found that although those sequences are very large, they are highly similar to each other. Thus it is feasible to reduce the space cost by storing their differences to a reference sequence. New studies show that it is possible to directly search on the compressed data. The target of this study is to improve the scalability of the indexing and searching techniques to meet the growing demand of big data. Based on the existing method, this work is placed on compressing the reference sequence. Several optimization techniques are proposed to perform efficient exact and approximate search with arbitrary query length on the compressed data. The process is further improved by utilizing parallel computing to crease the query efficiency for big data. Experimental study demonstrates the efficiency of the proposed method.
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基金项目:国家自然科学基金优秀青年基金(61322208);国家重点基础研究发展计划(973)(2012CB316201);国家自然科学基金(61272178,61572122,61532021) 国家自然科学基金优秀青年基金(61322208);国家重点基础研究发展计划(973)(2012CB316201);国家自然科学基金(61272178,61572122,61532021)
Foundation items:National Natural Science Foundation-Outstanding Youth Foundation (61322208); National Basic Research Program of China (973) (2012CB316201); National Natural Science Foundation of China (61272178, 61572122, 61532021)
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WANG Jia-Ying,WANG Bin,YANG Xiao-Chun.Efficient Compressed Genomic Data Oriented Query Approach.Journal of Software,2016,27(7):1715-1728