Improved Comb Filter based Approach for Effective Prediction of Protein Coding Regions in DNA Sequences

Meher, Jayakishan; Meher, Pramod Kumar; Dash, Gananath

doi:10.4236/jsip.2011.22012

Cited by 10 publications

(4 citation statements)

References 25 publications

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“…Table 3 summarizes the simulation results of the eight genes used as test data. It is evident from tabulated data that S n , S p and the average of S n and S p of the proposed method are significantly higher than existing method in all the cases whereas the miss rate and wrong rate are much lower indicating superior performance of the proposed algorithm over the existing technique [ 33 ].…”

Section: Resultsmentioning

confidence: 99%

Effective gene prediction by high resolution frequency estimator based on least-norm solution technique

Roy¹,

Barman

2014

J Bioinform Sys Biology

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Linear algebraic concept of subspace plays a significant role in the recent techniques of spectrum estimation. In this article, the authors have utilized the noise subspace concept for finding hidden periodicities in DNA sequence. With the vast growth of genomic sequences, the demand to identify accurately the protein-coding regions in DNA is increasingly rising. Several techniques of DNA feature extraction which involves various cross fields have come up in the recent past, among which application of digital signal processing tools is of prime importance. It is known that coding segments have a 3-base periodicity, while non-coding regions do not have this unique feature. One of the most important spectrum analysis techniques based on the concept of subspace is the least-norm method. The least-norm estimator developed in this paper shows sharp period-3 peaks in coding regions completely eliminating background noise. Comparison of proposed method with existing sliding discrete Fourier transform (SDFT) method popularly known as modified periodogram method has been drawn on several genes from various organisms and the results show that the proposed method has better as well as an effective approach towards gene prediction. Resolution, quality factor, sensitivity, specificity, miss rate, and wrong rate are used to establish superiority of least-norm gene prediction method over existing method.

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Section: Resultsmentioning

confidence: 99%

Effective gene prediction by high resolution frequency estimator based on least-norm solution technique

Roy¹,

Barman

2014

J Bioinform Sys Biology

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“…The existing signal processing methods such as discrete Fourier transform, digital filter such as notch filter and comb filter can effectively predict these regions. The comb filter has been choosen in this paper for its low computational complexity and better sensitivity and specificity [15].…”

Section: Prediction Of Protein Coding Regionsmentioning

confidence: 99%

Wavelet Based Lossless DNA Sequence Compression for Faster Detection of Eukaryotic Protein Coding Regions

Meher¹,

Panigrahi²,

Dash³

et al. 2012

IJIGSP

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Discrimination of protein coding regions called exons from noncoding regions called introns or junk DNA in eukaryotic cell is a computationally intensive task. But the dimension of the DNA string is huge; hence it requires large computation time. Further the DNA sequences are inherently random and have vast redundancy, hidden regularities, long repeats and complementary palindromes and therefore cannot be compressed efficiently. The objective of this study is to present an integrated signal processing algorithm that considerably reduces the computational load by compressing the DNA sequence effectively and aids the problem of searching for coding regions in DNA sequences. The presented algorithm is based on the Discrete Wavelet Transform (DWT), a very fast and effective method used for data compression and followed by comb filter for effective prediction of protein coding period-3 regions in DNA sequences. This algorithm is validated using standard dataset such as HMR195, Burset and Guigo and KEGG.

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“…The Exon regions reflect a period-3 property due to the existence of codon structure in protein synthesis process [4]. Several Digital signal Processing (DSP) methods have been reported by researchers to explore this period-3 property, such as: sliding DFT (STDFT) [5][6][7][8][9][10], digital filtering [11][12][13][14][15], continuous wavelet transform [16][17][18], discrete wavelet transform [19,20] and S-transform [21]. In this paper, the focus is given on digital filtering method.…”

Section: Introductionmentioning

confidence: 99%

“…Ramachandran et al [12] implemented the narrow band‐pass digital filter and low pass filter for exon region detection and reported lower computational time compared to STDFT [10] based approach. An improved comb filter‐based approach is reported in [13] for detection of Exon region with better prediction accuracy and less computational complexity. For the same problem, Hota and Srivastava [14] had used three anti‐notch IIR filters: conjugate suppression anti‐notch filter (suppresses the conjugate frequency component), anti‐notch filter followed by moving average filter (decrease the background noise) and harmonic suppression anti‐notch filter (removes the harmonic frequency component).…”

Section: Introductionmentioning

confidence: 99%

VLSI implementation of anti‐notch lattice structure for identification of exon regions in Eukaryotic genes

Pathak

Nanda

Joshi

et al. 2020

IET Computers & Digital Techniques

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In a Eukaryotic gene, identification of exon regions is crucial for protein formation. The periodic-3 property of exon regions has been used for its identification. An anti-notch infinite impulse response (IIR) filter is mostly employed to recognise this periodic-3 property. The lattice structure realisation of anti-notch IIR filter requires less hardware over direct from-II structures. In this study, a hardware implementation of IIR anti-notch filter lattice structure is carried out on Zynq-series (Zybo board) field programmable gate array (FPGA). The performance of hardware design has been improved using techniques like retiming, pipelining and unfolding and finally assessed on various Eukaryotic genes. The hardware implementation reduces the time frame to analyse the DNA sequence of Eukaryotic genes for protein formation, which plays a significant role in detecting individual diseases from genetic reports. Here, the performance evaluation is carried out in MATLAB simulation environment and the results are found similar. Application-specific integrated circuit (ASIC) implementation of the anti-notch filter lattice structure is also carried out on CADENCE-RTL compiler. It is observed that the FPGA implementation is 31 to 34 times faster and ASIC implementation is 58 to 64 times faster compared to the results generated by MATLAB platform with similar prediction accuracy.

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Improved Comb Filter based Approach for Effective Prediction of Protein Coding Regions in DNA Sequences

Cited by 10 publications

References 25 publications

Effective gene prediction by high resolution frequency estimator based on least-norm solution technique

Effective gene prediction by high resolution frequency estimator based on least-norm solution technique

Wavelet Based Lossless DNA Sequence Compression for Faster Detection of Eukaryotic Protein Coding Regions

VLSI implementation of anti‐notch lattice structure for identification of exon regions in Eukaryotic genes

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