基于功率谱分析的基因编码序列单碱基突变研究
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摘要
针对DNA序列单碱基的不同类型突变,利用数字信号处理方法,研究了单碱基替换突变、删除突变、插入突变对DNA序列三周期功率谱的影响。研究结果表明:对于不同长度的编码序列,替换突变对序列功率谱的影响较小,删除突变和插入突变对序列功率谱的影响较大;随着序列编码区长度的减小,替换、删除、插入突变对序列编码区的功率谱影响会越来越大。对于中等长度外显子,插入突变对序列三周期功率谱影响最大,对于短外显子,删除突变对序列三周期功率谱的影响最大。研究结果可为含突变基因编码区的识别与检测提供参考。
In view of the different mutations of single-base in DNA sequence, the effects of single base substitution mutation, deletion mutation and insertion mutation on triply periodic power spectrum of DNA sequences were investigated by using digital signal processing method. The results showed that for the coding sequences with different lengths, the substitution mutation had little effect on sequence power spectrum, but the effects of deletion mutation and insertion mutation on sequence power spectrum were larger. With the decrease of the length of the sequences in coding region, substitution mutation, deletion mutation and insertion mutation had a growing impact on the power spectrum of sequences in coding region. For the medium length exons, insertion mutation had the greatest impact on triply periodic power spectrum of the sequence. For the short exons, deletion mutation had the greatest impact on triply periodic power spectrum of the sequence. The results could provide references for the identification and detection of the coding region with mutant genes.
In view of the different mutations of single-base in DNA sequence, the effects of single base substitution mutation, deletion mutation and insertion mutation on triply periodic power spectrum of DNA sequences were investigated by using digital signal processing method. The results showed that for the coding sequences with different lengths, the substitution mutation had little effect on sequence power spectrum, but the effects of deletion mutation and insertion mutation on sequence power spectrum were larger. With the decrease of the length of the sequences in coding region, substitution mutation, deletion mutation and insertion mutation had a growing impact on the power spectrum of sequences in coding region. For the medium length exons, insertion mutation had the greatest impact on triply periodic power spectrum of the sequence. For the short exons, deletion mutation had the greatest impact on triply periodic power spectrum of the sequence. The results could provide references for the identification and detection of the coding region with mutant genes.
引文
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Voss R.F.,1992,Evolution of long-range fractal correlations and1/f noise in DNA base sequences,Physical Review Letters,68(25):3805-3808
Wu G.Y.,and Fang F.D.,eds.,1992,Gene diagnosis technology and application,Beijing Medical University and China Xie-He,Medical University Joint Publishing House,Beijing,China,pp.27-34(吴冠芸,方福德,编著,基因诊断技术及应用,北京医科大学,北京协和医科大学联合出版社,中国,北京,pp.27-34)
Wu G.Y.,and Wang S.W.,eds.,1988,Gene diagnosis,People's Medical Publishing House,Beijing,China,pp.22-52(吴冠芸,王申五,主编,1988,基因诊断,人民卫生出版社,中国,北京,pp.22-52)
Wang Z.,Chen Y.Z.,and Li Y.X.,2004,A brief review of computational gene prediction methods,Genomics,Proteomics&Bioinformatics,2(4):216-221
Yin C.,and Yau S.S.,2005,A Fourier characteristic of coding sequences:origins and a non-fourier approximation,Journal of Computational Biology,12(9):1153
Zhang R.,and Zhang C.T.,1994,Z curves,an intutive tool for visualizing and analyzing the DNA sequences,Journal of Biomolecular Structure&Dynamics,11(4):767-782
Akhtar M.,Epps J.,and Ambikairajah E.,2008,Signal processing in sequence analysis:advances in eukaryotic gene prediction,IEEE Journal of Select Topics in Signal Processing,2(3):310-321
MathéC.,Sagot M.F.,Schiex T.,and RouzéP.,2002,SURVEYAND SUMMARY:current methods of gene prediction,their strengths and weaknesses,Nucleic Acids Research,30(19):4103-4117
Marhon S.A.,and Kremer S.C.,2011,Gene prediction based on dna spectral analysis:a literature review,Journal of Computational Biology A Journal of Computational Molecular Cell Biology,18(4):639-676
Nair A.S.,and Sreenadhan S.P.,2006,A coding measure scheme employing electron-ion interaction pseudopotential(EIIP),Bioinformation,1(6):197-202
Saeys Y.,RouzéP.,and Van de P.Y.,2007,In search of the small ones:improved prediction of short exons in vertebrates,plants,fungi and protists,Bioinformatics,23(4):414-420
Tian Y.X.,Chen C.,Zou X.Y.,Qiu J.D.,Cai P.X.,and Mo J.Y.,2005,Study on period-3 behavior of exons,Huaxue Xuebao(Acta Chimica Sinica),63(13):1215-1219(田元新,陈超,邹小勇,邱健丁,蔡沛祥,莫金垣,2005,外显子周期三行为特征的研究,化学学报,63(13):1215-1219)
Tiwari S.,Ramachandran S.,Bhattacharya A.,Bhattacharya S.,and Ramaswamy R.,1997,Prediction of probable genes by Fourier analysis of genomic sequences,Bioinformatics,13(3):263-270
Voss R.F.,1992,Evolution of long-range fractal correlations and1/f noise in DNA base sequences,Physical Review Letters,68(25):3805-3808
Wu G.Y.,and Fang F.D.,eds.,1992,Gene diagnosis technology and application,Beijing Medical University and China Xie-He,Medical University Joint Publishing House,Beijing,China,pp.27-34(吴冠芸,方福德,编著,基因诊断技术及应用,北京医科大学,北京协和医科大学联合出版社,中国,北京,pp.27-34)
Wu G.Y.,and Wang S.W.,eds.,1988,Gene diagnosis,People's Medical Publishing House,Beijing,China,pp.22-52(吴冠芸,王申五,主编,1988,基因诊断,人民卫生出版社,中国,北京,pp.22-52)
Wang Z.,Chen Y.Z.,and Li Y.X.,2004,A brief review of computational gene prediction methods,Genomics,Proteomics&Bioinformatics,2(4):216-221
Yin C.,and Yau S.S.,2005,A Fourier characteristic of coding sequences:origins and a non-fourier approximation,Journal of Computational Biology,12(9):1153
Zhang R.,and Zhang C.T.,1994,Z curves,an intutive tool for visualizing and analyzing the DNA sequences,Journal of Biomolecular Structure&Dynamics,11(4):767-782