Calcutta Technical School

Kolkata, India

Calcutta Technical School

Kolkata, India
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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.


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.


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.


Barman S.,University of Calcutta | Biswas S.,University of Calcutta | Das S.,University of Calcutta | Roy M.,Calcutta Technical School
CODEC 2012 - 5th International Conference on Computers and Devices for Communication | Year: 2012

Gene prediction is an important topic in genomic research. Various techniques are in use for identification of protein coding regions in genes. Application of Fourier technique is one of the most popular methods of gene prediction, in which prediction algorithm is based on period-3 property of DNA where it exhibits a prominent peak in coding region. Spectrum estimation by Fourier method generates various harmonics, generally known as 1/f noise along with sharp peaks, which may lead to false prediction of coding regions. Researchers used various parametric and non-parametric filters to tackle this problem and improve the accuracy of prediction. Performance of anti-notch filter with cascaded lattice structure on one hand and harmonic suppressor with comb filter on the other hand have been compared here for identification of coding regions of C-elegan F56F11.4a chromosome. The authors have analyzed the performance in terms of standard deviation and signal-to-noise ratio. A Matlab simulink environment has been used for filter realization and performance analysis. © 2012 IEEE.


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.


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.


Mukhopadhyay B.,Central Calcutta Polytechnic | Bhattacharyya R.,Calcutta Technical School
Journal of Biological Systems | Year: 2011

In the present paper, we study a Prey-Predator-Pathogen model where the prey population suffer from an SI epidemic. The predator is assumed to exercise preferential predation. The prey preference mechanism ranges from predation only on the susceptible or only on the infective to proportional predation on both the prey types. The formulation maintains the native Holling type-II functional response in one hand and invokes prey switching on the other. We first describe stability and persistence results for the model without preference, which highlights the significance of some system parameters namely, predator mortality rate and predation pressure on the susceptible in shaping the system dynamics. Then we investigate the model with the preference mechanism, which shows the importance of the preference parameter (α) in controlling the stability and existence criteria of component populations. Our study reveals the existence of preference parameter ranges that (i) guarantees stable species coexistence (ii) exhibits rich dynamics in the form of oscillatory phenomena, point attractors and limit cycle attractors and (iii) causes possible extinction of the predators together with the susceptible prey. The ecological meaning of the corresponding ranges is also elaborated. © 2011 World Scientific Publishing Company.


Bhattacharyya R.,Calcutta Technical School | Mukhopadhyay B.,Central Calcutta Polytechnic
Nonlinear Analysis: Real World Applications | Year: 2010

In this paper, we study an eco-epidemiological model where prey disease is modeled by a Susceptible-Infected (SI) scheme. Saturation incidence kinetics is used to model the contact process. The predator population adapt switching technique among susceptible and infected prey. The prey species is supposed to be commercially viable and undergo constant non-selective harvesting. We study the stability aspects of the basic and the switching models around the infection-free state and the infected steady state from a local as well as a global perspective. Our aim is to study the role of harvesting and switching on the dynamics of disease propagation and/or eradication. A comparison of the local and global dynamical behavior in terms of important system parameters is obtained. Numerical simulations are done to illustrate the analytical results. © 2009 Elsevier Ltd. All rights reserved.


Bhattacharyya R.,Calcutta Technical School | Mukhopadhyay B.,Central Calcutta Polytechnic
Journal of Biological Physics | Year: 2011

In the present paper, we consider a mathematical model of ecosystem population interaction where the population suffers from a susceptible- infectious-susceptible disease. Dispersal of both the susceptible and the infective is incorporated using reaction-diffusion equations. We first study the stability criteria of the basic (non-spatial) model around the disease-free and the infected steady states. We find that the loss rate of the infective species controls disease prevalence. Also without predation pressure, the disease will continue to exist among the population. Then we analyze the spatial model with species dispersal in constant as well as in time-varying form. It is observed that though constant dispersal is unable to generate diffusion-driven instability, dispersal with sinusoidal variation in dispersion rate can generate diffusive instability when the wave number of the perturbation lies within a given range. Numerical simulations are performed to illustrate analytical studies. © Springer Science+Business Media B.V. 2011.


Mukhopadhyay B.,Central Calcutta Polytechnic | Bhattacharyya R.,Calcutta Technical School
Nonlinear Analysis: Real World Applications | Year: 2011

Stage-structured predatorprey models exhibit rich and interesting dynamics compared to homogeneous population models. The objective of this paper is to study the bifurcation behavior of stage-structured preypredator models that admit stage-restricted predation. It is shown that the model with juvenile-only predation exhibits Hopf bifurcation with the growth rate of the adult prey as the bifurcation parameter; also, depending on parameter values, a stable limit cycle will emerge, that is, the bifurcation will be of supercritical nature. On the other hand, the analysis of the model with adult-stage predation shows that the system admits a fold-Hopf bifurcation with the adult growth rate and the predator mortality rate as the two bifurcation parameters. We also demonstrate the existence of a unique limit cycle arising from this codimension-2 bifurcation. These results reveal far richer dynamics compared to models without stage-structure. Numerical simulations are done to support analytical results. © 2011 Elsevier Ltd. All rights reserved.

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