Browsing Division of Bioinformatics (DIC) by Issue Date
Now showing items 1-20 of 83
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Faculty Publication List : Dept. of Bioinformatics , 2000-01
(Bose Institute, 2001) -
Faculty Publication List : Dept. of Bioinformatics , 2001-02
(Bose Institute, 2002) -
Faculty Publication List : Dept. of Bioinformatics , 2002-03
(Bose Institute, 2003) -
Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis
(ELSEVIER SCIENCE, 2003-03-28)Genomic GC (overall G + C content of the coding sequences) variations were reinvestigated between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae species. It was observed that overall genomic ... -
Faculty Publication List : Dept. of Bioinformatics , 2003-04
(Bose Institute, 2004) -
Synonymous Codon Usage in Lactococcus lactis: Mutational Bias Versus Translational Selection
(ADENINE PRESS, 2004-02)In this study codon usage bias of all experimentally known genes of Lactococcus lactis has been analyzed. Since Lactococcus lactis is an AT rich organism, it is expected to occur A and/or T at the third position of codons ... -
Shannon's uncertainty principle and gene expression levels
(CURRENT SCIENCE, 2004-04-25)Shannon's uncertainty principle has been applied to measure the degree of constraints in codon bias in the coding sequences of Escherichia coli, Saccharomyces cerevisiae and Haemophilus influenzae. Our study shows a high ... -
Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M-smegmatis: Identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species
(SPRINGER SINGAPORE PTE LTD, 2004-07-31)The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were ... -
Evolutionary forces in shaping the codon and amino acid usages in Bochmannia floridanus
(ADENINE PRESS,, 2004-08)Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using ... -
Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis
(ADENINE PRESS,, 2004-10)Base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of Aquifex aeolicus and Bacillus subtilis, having different optimal growth temperatures. These two bacteria do not ... -
Faculty Publication List : Dept. of Bioinformatics, 2004-05
(Bose Institute, 2005) -
The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes
(ELSEVIER SCIENCE, 2005-01-17)Fluctuations and increments of both C-3 and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) ... -
Correlations between genomic GC levels and optimal growth temperatures: some comments
(ACADEMIC PRESS, 2005-02-25)Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed ... -
On the origin of genomic adaptation at high temperature for prokaryotic organisms
(ELSEVIER SCIENCE, 2005-05-13)For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures (T-opt). Long-standing ... -
Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"
(ELSEVIER SCIENCE, 2005-05-20)Recently Anders Fuglsang provided a modified way for calculating N-c when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each ... -
3(10)-Helix Adjoining a -Helix and b -Strand: Sequence and Structural Features and Their Conservation
(WILEY-BLACKWELL, 2005-06-15)Does the amino acid use at the terminal positions of an a-helix become altered depending on the context-more specifically. when there is an adjoining 3(10)-helix, and can a single helical cylinder encompass the resultant ... -
Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms
(ELSEVIER SCI, 2005-07)Correlations between genomic GC contents and amino acid frequencies were studied in the homologous sequences of 12 eubacterial genomes. Results show that amino acids encoded by GC-rich codons increases significantly with ... -
A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon
(ACADEMIC PRESS, 2005-09-23)Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse ... -
Conservation and relative importance of residues across protein-protein interfaces
(NATL ACAD SCIENCES, 2005-10-25)A core region surrounded by a rim characterizes biological interfaces. We ascertain the importance of the core by showing the sequence entropies of the residues comprising the core to be smaller than those in the rim. Such ... -
Faculty Publication List : Dept. of Bioinformatics, 2005-06
(Bose Institute, 2006)