Gene Prediction Based on All-phase Filtering Theories

Abstract

Abstract:

A novel design of FIR (finite impulse response) filter named APNPBF (all-phase narrow passband filter) was proposed based on all-phase theories. The APNPBF can provide the passband gain with high precision and can satisfy the required specifications without repeatedly modifying the design. The frequency sampling, Chebyshev window and all-phase narrow pass-band filters were applied as the kernel of the prediction algorithm of protein coding regions respectively. The prediction results measured with AC (approximate correlation) at the base level of DNA sequences from data sets HMR195 and ALLSEQ proved the superiority of the proposed method.

Key words：

Key words: all-phase, narrow pass-band filter, gene prediction, protein coding regions prediction, window function

CLC Number:

Q 751
TN 713

References

［1］Sitanshu S S, Ganapati P. Identification of proteincoding regions in DNA sequences using a timefrequency filtering approach ［J］. Genomics, Proteomics & Bioinformatics, 2011, 9(1): 4555.

［2］Chen B，Ji P. Visualization of the proteincoding regions with a self adaptive spectral rotation approach［J］. Nucleic Acids Research, 2011, 39(1):e3.

［3］Akhtar M, Epps J, Ambikairajah E. Signal processing in sequence analysis: advances in Eukaryotic gene prediction ［J］. IEEE Journal of Selected Topics in Signal Processing, 2008, 2(3): 310321.

［4］Tiwari S, Ramachandran S, Bhattacharya A, et al. Prediction of probable genes by Fourier analysis of genomic sequences ［J］. Computer Applications in the Bioscience, 1997, 13(3): 263270.

［5］Vaidyanathan P P, Yoon B J. Digital filters for gene prediction applications ［C］∥IEEE ThirtySix Asilomar Conference on Signals, Systems and Computers. Monterey, CA：［s.n.］ , 2002: 306310.

［6］Vaidyanathan P P, Yoon B J. Gene and exon prediction using allpassbased filters ［C］∥ Workshop on Genomic Signal Processing and Statistics. Raleigh, North Carolina, USA：［s.n.］， 2002.

［7］Meher J, Raval M K, Dash G, et al. Prediction of hydrophobic regions effectively in transmembrane proptins using digital filter ［J］. Journal Biomedical Science and Engineering, 2011, 4(8): 562568.

［8］Meher J K, Dash G N, Meher P K,et al. A reduced computational load protein coding predictor using equivalent amino acid sequence of DNA string with period3 based time and frequency domain analysis ［J］. American Journal of Molecular Biology, 2011, 1(2): 7986.

［9］Meher J, Meher P K, Dash G. Improved comb filter based approach for effective prediction of protein coding regions in DNA sequences ［J］. Journal of Signal and Information Processing, 2011, 2(2): 8899.

［10］马宝山，朱义胜. 一种用于基因预测的FIR数字滤波器［J］. 电子学报, 2007，35(9)：17101713.

MA Baoshan, ZHU Yisheng. FIR digital filter for gene prediction application ［J］. ACTA Electronica sinica, 2007, 35(9): 17101713.

［11］马玉韬，车进，关欣，等.加窗窄通带滤波器蛋白质编码区预测算法［J］. 数据采集与处理，2013，28（2）：129135.

MA Yutao, CHE Jin, GUAN Xin, et al. Prediction Algorithm for protein coding regions based on windowed narrow passband filter［J］.Journal of Data Acquisition & Processing, 2013, 28 (2): 129135.

［12］MenaChalco J P, Carrer H, Zana Y, et al. Identification of protein coding regions using the modified GaborWavelet transform ［J］. IEEE/ACM Transactions on Computational biology and bioinformatics, 2008, 5(2): 198206.

［13］胡广书. 数字信号处理——理论算法与实现［M］. 2版.北京: 清华大学出版社, 2003.

［14］侯正信，徐妮妮. 加窗全相位DFT数字滤波器［J］. 天津大学学报，2005，38(5)：448454.

HOU Zhengxin, XU Nini. Windowed allphase DFT digital filter ［J］. Journal of Tianjin University, 2005，38 (5)：448454.

［15］黄翔东，王兆华. 基于两种频率对称采样的全相位FIR滤波器设计［J］. 电子与信息学报，2007,29(2)：478481.

HUANG Xiangdong, WANG Zhaohua. Allphase FIR filter design based on two kinds of symmetric frequency sampling［J］. Journal of Electronics & Information Technology, 2007, 29(2): 478481.

［16］黄翔东，王兆华，吕卫. 陷波频率点可精确控制的高效FRM陷波器设计［J］. 系统工程与电子技术， 2009,31(10)：23202322, 2454.

HUANG Xiangdong, WANG Zhaohua, LV Wei. Design of highefficiency FRM notch filter with frequency point accurately controlled ［J］. Systmes Engineering and Electronics, 2009, 31(10)：23202322.

［17］Burset M, Guigo R. Evaluation of gene structure prediction programs ［J］. Genomics, 1996, 34(3): 353367.

［18］Rogic S, Mackworth A K , Ouellette B F . Evaluation of GeneFinding Programs on Mammalian Sequences ［J］. Genome Research, 2001, 11(5): 817832.

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