Improved gene prediction by principal component analysis based autoregressive Yule–Walker method

• Objective is to identify protein coding regions in gene using period-3 peaks.
• Initially map DNA sequence into digital signal then apply parametric technique of power spectral estimation.
• The problem of parametric method is accurate choice of model order.
• Apply autoregressive Yule-Walker method combined with Principal Component Analysis so that model order selection is no more critical, as noise is removed beforehand.
• Period-3 peaks obtained are sharper.

Spectral analysis using Fourier techniques is popular with gene prediction because of its simplicity. Model-based autoregressive (AR) spectral estimation gives better resolution even for small DNA segments but selection of appropriate model order is a critical issue. In this article a technique has been proposed where Yule–Walker autoregressive (YW-AR) process is combined with principal component analysis (PCA) for reduction in dimensionality. The spectral peaks of DNA signal are used to detect protein-coding regions based on the 1/3 frequency component. Here optimal model order selection is no more critical as noise is removed by PCA prior to power spectral density (PSD) estimation. Eigenvalue-ratio is used to find the threshold between signal and noise subspaces for data reduction. Superiority of proposed method over fast Fourier Transform (FFT) method and autoregressive method combined with wavelet packet transform (WPT) is established with the help of receiver operating characteristics (ROC) and discrimination measure (DM) respectively.

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