Siddhartha Sankar Satapathy

Siddhartha Sankar Satapathy
Tezpur University · Department of Computer Science & Engineering

PhD

About

39
Publications
3,869
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311
Citations
Citations since 2016
18 Research Items
181 Citations
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2016201720182019202020212022010203040
2016201720182019202020212022010203040
2016201720182019202020212022010203040

Publications

Publications (39)
Preprint
The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting higher rate of C>T transitions. Intra-operon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas inter-operon intergenic...
Article
Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high and the low expression genes in organisms is not yet adequately reported across different bacteria. In this study, a machine learning based approach was implemented initially to find out codons that are significantly different betwee...
Article
Full-text available
A common approach to estimate the strength and direction of selection acting on protein codingsequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still ev...
Preprint
The previous findings suggest that replication and transcription are two major reasons behind the different substitution patterns of mutations in genomic DNA. In the current work, we have compared the adjacent co-transcribed gene pairs regarding synonymous polymorphism in five different operons in Escherichia coli. It is interesting that the co-tra...
Article
Full-text available
Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition i...
Preprint
The dN/dS value is estimated in homologous protein coding gene sequences between two closely related organisms for studying selection on the genes. In the usual method of calculation of synonymous (S) and non-synonymous (NS) sites in codons, the transition and transversion rates are considered same as well as no difference of pretermination codons...
Preprint
Full-text available
We investigated single nucleotide polymorphism in intergenic regions (IRs) and four-fold degenerate sites (FFS) in genomes of three γ-Proteobacteria and two Firmicutes to understand the mechanism of nucleotide compositional asymmetry between the leading and the lagging strands. Pattern of the polymorphism spectra were alike regarding transitions bu...
Article
Ralstonia solanacearum causes a lethal bacterial wilt disease in many plants by colonizing the vascular tissues of the hosts. Upon inoculation of tomato seedlings either through leaf or root, the wilting symptoms occur first at the apical region and then proceed downward along the shoot. The systemic order of the disease initiation and progression...
Article
Full-text available
Understanding the metabolic versatility of Ralstonia solanacearum is important, as it regulates the trade-off between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on the potential roles of glycolysis and the oxidative pentose phosphate pat...
Preprint
In Ralstonia solanacearum , a devastating phytopathogen whose metabolism is poorly understood, we observed that Entner-Doudoroff (ED) pathway and NonOxidative pentose phosphate pathway (OxPPP) bypasses glycolysis and OxPPP under glucose oxidation. Evidences derived from ¹³ C stable isotopes feeding and genome annotation based comparative metabolic...
Article
Effective number of codons (N^c) and its variant N^'c (effective number of codons prime) are the two widely used methods for measuring unequal usage of synonymous codons in coding sequences, known as the codon usage bias (CUB). The mathematical formula used in calculating N^c and N^'c values is giving inappropriate measures of CUB in case of low ab...
Article
Full-text available
The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons...
Chapter
Resource constrained low-cost sensor nodes deployed in large scale are the potential source of information in wireless sensor networks (WSN). Usually, sensor nodes are equipped with a non-rechargeable battery, which is having limited power and therefore its judicious use is essential for longer network life. Data gathering protocols proposed in the...
Article
Full-text available
To decode all the 61 sense codons in the genetic code, the number of different anticodons used in bacteria varies between 24 to 45. If a small set of anticodon can decode all the codons in a bacterium, the evolutionary significance of the increase in anticodon diversity in a bacterium is not understood well. The higher anticodon diversity in G+C% h...
Article
The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G + C% of the HEG was found to be less in comparison to t...
Article
Due to the degeneracy in the genetic code, many amino acids are encoded by more than one codon, called synonymous codons. The usage of synonymous codons in a coding sequence is not random, a phenomenon known as codon usage bias (CUB) that occurs in all genomes. It is believed that synonymous codons are not equivalent with respect to their coding ef...
Article
It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative...
Article
The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across...
Article
Full-text available
It is generally believed that the effect of translational selection on codon usage bias is related to the number of transfer RNA genes in bacteria, which is more with respect to the high expression genes than the whole genome. Keeping this in the background, we analyzed codon usage bias with respect to asparagine, isoleucine, phenylalanine, and tyr...
Article
Full-text available
Next generation wireless network is foreseen as the combination of heterogeneous wireless networks capable of providing enhanced services to mobile users. Vertical handoff is a crucial issue in providing service to mobile users, in a heterogeneous network. To maintain continuous service during vertical handoff period, the handoff procedure should c...
Article
Next generation wireless network is foreseen as the combination of heterogeneous wireless networks capable of providing enhanced services to mobile users. Vertical handoff is a crucial issue in providing service to mobile users, in a heterogeneous network. To maintain continuous service during vertical handoff period, the handoff procedure should c...
Article
Wireless sensor networks are usually deployed for gathering data from unattended or hostile environment. Several application specific sensor network data gathering protocols have been proposed in research literatures. However, most of the proposed algorithms have given little attention to the related security issues. In this paper we have explored...
Article
We have done a comparative study of tRNA diversity and total tRNA genes among different strains of bacteria with respect to the optimum growth temperature of the cells. Our observation suggests that higher tRNA diversity usually occurs in thermophiles in comparison to non-thermophiles. Among psychrophiles total tRNA was observed to be more than two...
Article
Full-text available
Chargaff's rule of intra-strand parity (ISP) between complementary mono/oligonucleotides in chromosomes is well established in the scientific literature. Although a large numbers of papers have been published citing works and discussions on ISP in the genomic era, scientists are yet to find all the factors responsible for such a universal phenomeno...
Conference Paper
Full-text available
Wireless sensor network (WSN) is usually used in civil and military applications for gathering data from the surrounding environment. As WSN is a self configured network and mostly works in an unattended wireless environment, there is a lot of scope for the adversaries to tamper the sensed data as well as may try to alter the underlying working pri...
Article
Mainly two selective forces are thought to affect transfer RNA (tRNA) gene numbers in cells: firstly, transfer RNA genes have coevolved with codon usage to optimize the translation rate in organisms; and secondly, tRNA gene number is positively correlated with growth rate of organisms. Since a codon ending with 'G' is recognized with lower efficien...
Conference Paper
Limited battery powers of sensor nodes demand routing protocol for sensor network that consume minimum possible amount of energy and hence give longer life to the system. In a sensor network, sensor nodes are the potential source of information and they need to send their sensed/collected information to a remote base station (BS)/Sink. Generally, i...
Article
Full-text available
Computational analysis of seven bacterial genomes revealed that both the DNA strands in a genome exhibit compositional symmetry in terms of the abundance of a non-palindromic oligonucleotide (di, tri, tetra, penta, hexa, hepta and octa). This symmetry in DNA duplex suggests that both strands in the duplex possess similar compositional characteristi...

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Projects

Projects (2)
Project
This project is to reconstruct genome scale metabolic networks of the plant pathogen R. solanacearum by using Metabolic flux analysis based on 13C-fluxomics and flux balance analysis. The project duration is for three years. Interested Indian national bioinformaticians my contact us for JRF/SRF positions.
Project
We are interested to know what are the factors involved in selecting a particular codon out of the synonymous codons in an organism. We are right now working on genomes of bacteria.