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Gene prediction by the noise-assisted MEMD and wavelet transform for identifying the protein coding regions

Zheng Qian, Chen Tao, Zhou Wenxiang, Xie Lei, Su Hongye

Biocybernetics and Biomedical Engineering

2021

Vol. 41, no. 1

196--210

The analysis of protein coding regions of DNA sequences is one of the most fundamental applications in bioinformatics. A number of model-independent approaches have been developed for differentiating between the protein-coding and non-protein-coding regions of DNA. However, these methods are often based on univariate analysis algorithms, which leads to the loss of joint information among four nucleotides of DNA. In this article, we introduce a method on basis of the noise-assisted multivariate empirical mode decomposition (NA-MEMD) and the modified Gabor-wavelet transform (MGWT). The NA-MEMD algorithm, as a multivariate analysis tool, is utilized to reconstruct the numerical analyzed sequence since it enables a matched-scale decomposition across all variables and eliminates the mode mixing. By virtues of NA-MEMD, the MGWT method achieves a stable improvement on the general identification performance. We compare our method with other Digital Signal Processing (DSP) methods on two representative DNA sequences and three benchmark datasets. The results reveal that our method can enhance the spectra of the analyzed sequences, and improve the robustness of MGWT to different DNA sequences, thus obtaining higher identification accuracies of protein coding regions over other applied methods. In addition, another comparative experiment with the model-dependent method (AUGUSTUS) on the recently proposed benchmark dataset G3PO verifies the superiority of model-independent methods (especially NA-MEMD-MGWT) for identifying coding regions of the poor-quality DNA sequences.

A new numerical approach for DNA representation using modified Gabor wavelet transform for the identification of protein coding regions

Raman Kumar M., Vaegae Naveen Kumar

Biocybernetics and Biomedical Engineering

2020

Vol. 40, no. 2

836--848

The fundamental step in genomic signal processing applications is to assign mathematical descriptor to nucleotides {A, T, G, C} of DNA molecule for discrete representation. The discrete representation should replicate biological information of gene when analyzed with digital signal processing tools. In this aspect, a novel binary representation of DNA sequence by combining structural and chemical information of original DNA sequence has been proposed for the identification of protein coding regions of eukaryotes. The identification model comprises two stages, mainly, numerical encoding in first stage, and analysis of biological behavior through digital signal processing algorithms in second stage. In the first stage, a new numerical encoding method based on Walsh codes of order-4 is proposed to obtain 1-D binary discrete sequence. In the second stage, the modified Gabor wavelet transform (MGWT) is employed on the discretized DNA sequence for spectrum analysis. The optimal gene numerical encoding and multiresolution approach of MGWT has readily identified the structures of coding regions of unknown gene sequences. The proposed model is validated by analyzing prediction efficiency in terms of statistical metrics such as sensitivity, specificity, accuracy on both sequence and data base level. Furthermore, the results are compared by plotting receiver operating curves (ROC) for all classification thresholds for the state-of-art encoding methods. Area under curve (AUC) value of 0.86 at sequence level and 0.84 at database level is achieved. Performance metrics indicate that the proposed encoding method exhibits relatively better performance than other numerical encoding methods.