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基于粒子群优化的支持向量机算法识别人类基因启动子

Recognition of gene promoters in human beings based on the particle swarm optimized support vector machine algorithm
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摘要 人类基因启动子识别是医学研究的基本需要。提取DNA序列碱基的PZ曲线特征、二核苷酸空间结构特征、保守信号似然得分,以及K联体似然得分,结合GC含量变化和非均匀指数,构建基于粒子群优化的支持向量机算法来识别人类基因启动子。利用粒子群优化支持向量机参数进行优化避免了人为选择的随机性,并且在分类问题中表现出较好的稳健性。对测试集的10-折交叉检验结果为:敏感性为92%,特异性为91%,马修斯关联系数为0.83。该结果表明,基于粒子群优化的支持向量机算法能有效识别启动子序列。 Recognition of gene promoters in human beings is a basic requirement for medical research. It was achieved through analysis of phase-specific PZ curves of nucleotide, spatial structure of nucleotide, conservative signal and K-mer likelihood score in DNA sequence, as well as GC content changes and in-homogeneity index. The support vector machine algorithm based-particle swarm optimization was proposed to identify human gene promoters. Using PSO algorithm to optimize the parameters of SVM can avoid the randomness of artificial selec- tion and present better robustness in classification. The sensitivity, specificity and MCC tested by the 10-fold cross-validation were 92%, 91%, and 0.83, respectively. The result indicated that PSO-SVM method can be used to effectively identify promoter sequences.
作者 张文 陈园园 张瑾 骈聪 李琴 张良云
机构地区 南京农业大学理学院
出处 《安徽农业大学学报》 CAS CSCD 北大核心 2015年第2期310-315,共6页 Journal of Anhui Agricultural University
基金 教育部博士点基金(20100097110040) 中央高校基本科研业务费专项资金(KYZ201125) 江苏省自然科学基金(BK20140676 BK20141358)共同资助
关键词 相位特异PZ曲线 粒子群优化 支持向量机 启动子预测 phase-specific PZ curve particle swarm optimization （PSO） support vector machine （SVM） promoter prediction
分类号 Q811.4 [生物学—生物工程]
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参考文献17

  • 1Reese M G. Application of a time-delay neural network topromoter annotation in the Drosophila melanogaster ge-nome[J]. Comput Chem, 2001,26(1): 51-56.
  • 2Bajic V B, Seah S H, Chong A, et al. Dragon PromoterFinder: recognition of vertebrate RNA polymerase IIpromoters[J]. Bioinformatics, 2002, 18(1): 198-199.
  • 3Scherf M, Klingenhoff A, Werner T. Highly specific lo-calization of promoter regions in large genomic sequencesby Promoter Inspector: a novel context analysis approach[J]. J Mol Biol, 2000,297(3): 599-606.
  • 4Gangal R, Sharma P. Human pol II promoter prediction:time series descriptors and machine learning [J]. NucleicAcids Res, 2005, 33(4): 1332-1336.
  • 5吕军,罗辽复.人类polⅡ启动子的识别[J].生物化学与生物物理进展,2005,32(12):1185-1191. 被引量：26
  • 6Tao L, Chen H, Xu Y, et al. A new promoter recognitionmethod based on features optimal selection[C]//Bioinformaticsand Biomedical Engineering, (iCBBE) 2011 5th InternationalConference on. IEEE, 2011:1-4.
  • 7Davuluri R V, Grosse I,Zhang M Q. Computational iden-tification of promoters and first exons in the human ge-nome [J]. Nat Genet, 2001, 29(4): 412-417.
  • 8Narang V,Sung W K,Mittal A. Computational modelingof oligonucleotide positional densities for human pro-moter prediction [J]. Artif Intell Med, 2005, 35(1):107-119.
  • 9Bajic V B,Tan S L,Suzuki Y,et al. Promoter predictionanalysis on the whole human genome [J]. Nat Biotechnol,2004,22(11): 1467-1473.
  • 10Zeng J, Zhao X Y,Cao X Q, et al. SCS: Signal, context,and structure features for genome-wide human promoterrecognition[J]. IEEE ACM Trans Comput Biol Bioinform,2010,7(3): 550-562.

二级参考文献45

  • 1桑海峰,何大阔,张大鹏.基于支持向量机与遗传算法的发酵过程软测量建模[J].东北大学学报（自然科学版）,2007,28(6):781-784. 被引量：12
  • 2SHI Y H, EBERHART R C. Parameter Selection in Particle Swarm Optimization [ C ]//Proceedings of the Seventh Annual Conf. on Evolutionary Programming [ C]. New York: Springer-Verlag, 1998. 591 -60!.
  • 3SHI Y H, EBERHART R C. A Modified Particle Swarm Optimizer [ C]//IEEE International Conference on Evolutionary Computation. Anchorage, Alaska: IEEE Press, 1998. 69 -73.
  • 4Xie X H, Lu J, Kulbokas E J, et al. Systematic discovery of regulatory motifs in humanpromoters and 3′UTRs by comparison of several mammals. Nature, 2005, 434 (7031): 338～345
  • 5Laxton R R. The measure of diversity. J Theor Biol, 1978, 71(1):51～67
  • 6McLachlan G J. Discriminant Analysis and Statistical Pattern Recognition. New York:Wiley, 1992. 1～526
  • 7Zhang M Q. Identification of protein coding regions in the human genome by quadraticdiscriminant analysis. Proc Natl Acad Sci USA, 1997, 94 (2): 565～568
  • 8Zhang L R, Luo L F. Splice site prediction with quadratic discriminant analysis usingdiversity measure. Nucleic Acids Research, 2003, 31(21): 6214～6220
  • 9Schmid C D, Praz V, Delorenzi M, et al. The eukaryotic promoter database EPD: theimpact of in silico primer extension. Nucleic Acids Research, 2004, 32:D82～85
  • 10Matthias S, Andreas K, Kornelie F, et al. First pass annotation of promoters on humanchromosome 22. Genome Res, 2001, 11 (3):333～340

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安徽农业大学学报
2015年 第2期

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