基因预测算法中阈值的傅里叶质谱分析.docVIP

基因预测算法中阈值的傅里叶质谱分析 　　摘要：蛋白质编码区预测中阈值选择对预测结果的影响不容忽视。研究提出以归一化的功率谱密度作为判别DNA序列编码区和非编码区的阈值，以FIR（Finite impulse response，FIR）窄通带滤波器NPBF（Narrow pass band filter，NPBF）作为编码区预测算法核心，采用DNA序列集HMR195和ALLSEQ作为测试集，以碱基层的近似相关系数 （Approximate correlation，AC）为预测准确率测度指标，对所提出方法与现有方法的预测结果做了比较。结果表明，采用新阈值得到的预测准确率最高，算法简单直观。 　　关键词：蛋白质编码区预测；窄通带滤波器；归一化的功率谱密度值；信噪比；近似相关系数 　　中图分类号：TP391.9；TN713 文献标识码：A 文章编号：0439-8114（2014）06-1432-04 　　Analysis on Threshold Used in Gene Prediction Algorithm Based on Fourier Spectrum 　　LIU Ping1，MA Yu-tao1，SUN Xue-hong1，ZHANG Cheng1，DU Yong2 　　（1.School of Physics Electrical Information Engineering/Ningxia Key Laboratory of Intelligent Sensing for Desert Information， Ningxia University，Yinchuan 750021，China；2.Department of Pediatric Surgery，General Hospital of Ningxia Medical University，Yinchuan 750004，China） 　　Abstract： Threshold selection of protein coding regions prediction algorithm has important influence on the prediction accuracy. In this paper， a new threshold and normalized value of power spectrum density was proposed to differentiate protein coding regions and non-coding regions. Using the FIR （Finite impulse response） NPBF （Narrow pass-band filter） as the kernel of the prediction algorithm and taking the DNA sequences data sets HMR195 and ALLSEQ as the test sets， the prediction results of the NPBF algorithm with new threshold was compared with those of the same algorithm using other two thresholds. The results were discussed with the AC（Approximate correlation） used as a base level prediction accuracy measure. It was indicated that the proposed threshold was the best choice for higher AC and less amount of computation. 　　Key words： protein coding regions prediction； narrow pass-band filter； normalized value of power spectrum density； ratio of signal to noise； approximate correlation 　　蛋白质编码区预测对于DNA序列的注释和标注工作具有很重要的指导意义[1-3]。在现有的蛋白质编码区预测算法中，Tiwari等[4]提出的SDFT（Sliding discrete fourier transform，SDFT）算法使用了信噪比RSN（Ratio of signal to noise，RSN）作为区分编码区和非编码