A multirate DSP structure for the identification of protein-coding regions

The identification of protein-coding regions in DNA sequence using digital signal processing methods is one of the central issues in bioinformatics. In this paper, a multirate structure is proposed for the identification of protein-coding regions whose input sampling rate is same as output sampling rate. The multirate structure consists of cascade combination of decimation filter, kernel filter and interpolation filter. The decimation filter is a complex filter, the kernel filter is an FIR lowpass filter and the interpolation filter isa moving average filter. Polyphase decomposition is applied on both decimation filter and interpolation filter for computationally efficient implementation. The potential of the proposed method is evaluated in comparison with existing methods using standard datasets. The results show that the proposed method improves the identification accuracy of protein-coding regions to a great extent compared to its counterparts.

Spectrum and symbol distribution of nucleotide sequences

This paper explores the connection between the size of the spectral coefficients of a nucleotide or any other symbolic sequence and the distribution of nucleotides along certain subsequences. It explains the connection between the nucleotide distribution and the size of the spectral coefficients, and gives a necessary and sufficient condition for a coefficient to have a prescribed magnitude. Furthermore, it gives a fast algorithm for computing the value of a given spectral coefficient of a nucleotide sequence, discussing periods 3 and 4 as examples. Finally, it shows that the spectrum of a symbolic sequence is redundant, in the sense that there exists a linear recursion that determines the values of all the coefficients from those of a subset.