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基于生物信息学特征的DNA序列数据压缩算法 被引量：8

Bioinformatics Features Based DNA Sequence Data Compression Algorithm
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摘要 本文通过将生物学特征和生物学含义引入DNA序列数据的压缩处理中,提出了基于生物信息学特征的BioLZMA压缩算法.在BioLZMA算法中,DNA序列根据组成部分生物学含义的不同切分重组为四个集合:编码序列CDS集合、内含子序列集合、RNA序列集合以及剩余序列的集合.根据各集合中序列的具体生物学特征分别使用针对性的压缩策略进行预处理,并通过LZMA算法进行压缩编码.实验结果表明,BioLZMA算法在基准测试序列上的压缩性能优于原有的DNA序列压缩方法.特别是对于生物信息学特征清晰的长序列,算法能够在较短的时间内获得较高的压缩率. A novel bioinformatics features based DNA Sequence data compression algorithm of BioLZMA is proposed in this paper.In BioLZMA,the DNA sequence data is sliced and reformed into 4 clusters according with biological meanings：the coding sequence cluster,the intron cluster,the RNA cluster and the residual cluster.By employing pointed compression strategies in data pre-processing,the clusters are compressed separately with LZMA algorithm.Experimental results demonstrated the better performance of BioLZMA than original DNA compression algorithms on benchmark sequences.Especially on long DNA sequence with significant bioinformatics features,BioLZMA algorithm can achieve higher compression ratio with little computation time.
作者 纪震 周家锐 朱泽轩 Q H Wu
机构地区 深圳大学计算机与软件学院 浙江大学生物医学工程与仪器科学院 利物浦大学电气电子工程系
出处 《电子学报》 EI CAS CSCD 北大核心 2011年第5期991-995,共5页 Acta Electronica Sinica
基金 国家自然科学基金(No.60872125) 霍英东教育基金会高等院校青年教师基金基础性研究课题 深圳市基础研究项目(杰青奖) 广东省自然科学基金
关键词 DNA数据压缩 生物信息学 序列重组 近似重复片段 LZMA DNA sequence data compression bioinformatics sequence regroup approximate repeat fragment Lempel-Ziv-Markov chain algorithm（LZMA）
分类号 TP391 [自动化与计算机技术—计算机应用技术]
  • 相关文献

参考文献15

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二级参考文献22

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共引文献6

同被引文献86

  • 1王玉,饶妮妮,匡斌,袁祚涌.基于小波变换技术预测DNA序列的编码区[J].电子学报,2007,35(1):141-144. 被引量：6
  • 2林毅申,林丕源,彭宏.基于字典的DNA序列压缩算法研究及应用[J].计算机应用研究,2007,24(6):265-267. 被引量：4
  • 3周家锐,纪震,等.基于自适应智能单粒子优化算法的Gabor人脸识别方法[A].全国模式识别学术会议[C].重庆:CCPR,2010.359-363.
  • 4张丽霞,张义青,林丕源,刘吉平.基于字符和0/1码的DNA压缩模式匹配算法[J].计算机应用研究,2007,24(9):22-24. 被引量：3
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  • 7Korodi G, Tabus I, et al. DNA sequence compression-based on the normalized maximum likelihood model IEEE Signal Processing Maga- zine, 2007 ; 24 ( 1 ) :47-53.
  • 8Galpedn M Y, Cochrane G R. Petabyte-scale innovations at the European nucleotide archive[J]. Nucleic Acids Research, 2009, 37:D1 - D4.
  • 9Srinivasa K G, Jagadish M, et al. Efficient compression of non- repetitive DNA sequences using dynamic programming [ A ]. Proceeding of International Conference on Advanced Comput- ing and Communications [ C ]. Mangalore: ADCOM, 2006. 569 - 574.
  • 10Chen X, Kwong S, et al. A compression algorithm for DNA se- quences and its applications in genome comparison[ A ]. Pro- ceeding of the 10th Workshop on Genome Informafics[ C]. Tokyo: GIW, 1999.51 - 61.

引证文献8

二级引证文献15

电子学报
2011年 第5期

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