Entity

Time filter

Source Type

Kolkata, India

Barman S.,University of Calcutta | Saha S.,University of Calcutta | Mandal A.,University of Calcutta | Roy M.,Calcutta Technical School
2012 International Conference on Informatics, Electronics and Vision, ICIEV 2012 | Year: 2012

Accurate exon prediction in a genome is extremely important for understanding of life processes. Researchers use various techniques for detecting accurate location of exons. A digital filter model has been proposed in this paper for the prediction of exons in DNA sequence. The technique involves conversion of DNA character string into a numerical sequence using weak-strong bonding of nucleotides and filtering the transformed sequence using Narrow Band Pass FIR filter whose passband is centered at 2π/3. The filtered signal power of Narrow band pass FIR filter is then used as a measure parameter for both exons and introns. A plot of signal power versus nucleotide location is used to distinguish exons from introns of a DNA sequence. The simulation plots show very distinct peaks in exon regions indicating its presence where as such peaks are absent in intron regions. The design model is tested for several databases of Homo sapiens Beta-globin chromosome which have been downloaded from National Center for Biotechnology Information (NCBI) homepage. © 2012 IEEE. Source


Roy M.,Calcutta Technical School | Barman S.,University of Calcutta
Eurasip Journal on Bioinformatics and Systems Biology | Year: 2014

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. © 2014 Roy and Barman; licensee Springer. Source


Mukhopadhyay B.,Central Calcutta Polytechnic | Bera A.,Shyamabzar A.V. School | Bhattacharyya R.,Calcutta Technical School
International Journal of Biomathematics | Year: 2010

In this paper, a food-chain model in a mangrove ecosystem with detritus recycling is analyzed. From the stability analysis of the delayed homogeneous system, an interval for the parameter representing detritus-detritivores interaction rate is obtained that imparts stability to the system around the coexistent state. Next, we have studied the model in a nonhomogeneous environment. The analysis revealed the existence of a subinterval of the above mentioned interval such that when the above interaction-rate lies within this interval, the system will undergo diffusion driven instability. Finally, we show the existence of travelling wave solutions for the said ecosystem. Numerical simulations are carried out to augment analytical results. © 2010 World Scientific Publishing Company. Source


Mukhopadhyay B.,Central Calcutta Polytechnic | Bhattacharyya R.,Calcutta Technical School
Applications of Mathematics | Year: 2010

We consider a mathematical model of nutrient-autotroph-herbivore interaction with nutrient recycling from both autotroph and herbivore. Local and global stability criteria of the model are studied in terms of system parameters. Next we incorporate the time required for recycling of nutrient from herbivore as a constant discrete time delay. The resulting DDE model is analyzed regarding stability and bifurcation aspects. Finally, we assume the recycling delay in the oscillatory form to model the daily variation in nutrient recycling and deduce the stability criteria of the variable delay model. A comparison of the variable delay model with the constant delay one is performed to unearth the biological relevance of oscillating delay in some real world ecological situations. Numerical simulations are done in support of analytical results. Source


Roy M.,Calcutta Technical School | Barman S.,University of Calcutta
Proceedings of the 2012 International Conference on Communications, Devices and Intelligent Systems, CODIS 2012 | Year: 2012

Digital Spectral Analysis of DNA sequence using AR Models have long been proved to be superior to classical Fourier Transform techniques. Here authors have applied a special case of all-pole model using Prony's method to DNA sequence from various Chromosomes for Power Spectral Density (PSD) estimation in order to identify protein-coding regions. A quaternary mapping method comprising real and imaginary values towards nucleotide bases has been employed. The simulation results obtained by Prony's model clearly show the demarcation between coding and non-coding regions of DNA sequence. © 2012 IEEE. Source

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