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Please use this identifier to cite or link to this item: http://krishi.icar.gov.in/jspui/handle/123456789/34084
Title: Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context
Other Titles: Not Available
Authors: Mohammad Samir Farooqi
DC Mishra
Niyati Rai
DP Singh
Anil Rai
K. K. Chaturvedi
Ratna Prabha
Manjeet Kaur
ICAR Data Use Licennce: http://krishi.icar.gov.in/PDF/ICAR_Data_Use_Licence.pdf
Author's Affiliated institute: ICAR::Indian Agricultural Statistics Research Institute
ICAR-National Bureau of Agriculturally Important Microorganisms
Published/ Complete Date: 2016-01-01
Project Code: Not Available
Keywords: Codon Usage Bias (CUB)
Halophilic bacteria
Relative
Publisher: Not Available
Citation: Farooqi MS, Mishra DC, Rai N, Singh DP, Rai A, et al. (2016) Genome-Wide Relative Analysis of Codon Usage Bias and Codon Context Pattern in the Bacteria Salinibacter Ruber, Chromohalobacter Salexigens and Rhizobium Etli. Biochem Anal Biochem 5: 257. doi:10.4172/2161-1009.1000257
Series/Report no.: Not Available;
Abstract/Description: Codon is the basic unit for biological message transmission during synthesis of proteins in an organism. Codon Usage Bias is preferential usage among synonymous codons, in an organisms. This preferential use of a synonymous codon was found not only among species but also occurs among genes within the same genome of a species. This variation of codon usage patterns are controlled by natural processes such as mutation, drift and pressure. In this study, we have used computational as well as statistical techniques for finding codon usage bias and codon context pattern of Salinibacter ruber (extreme halophilic), Chromohalobacter salexigens (moderate halophilic) and Rhizobium etli (nonhalophilic). In addition to this, compositional variation in translated amino acid frequency, effective number of codons and optimal codons were also studied. A plot of ENc versus GC3s suggests that both mutation bias and translational selection contribute to these differences of codon bias. However, mutation bias is the driving force of the synonymous codon usage patterns in halophilic bacteria (Salinibacter ruber and Chromohalobacter salexigens) and translational selection seems to affect codon usage pattern in non-halophilic bacteria (Rhizobium etli). Correspondence analysis of Relative Synonymous Codon Usage revealed different clusters of genes varying in numbers in the bacteria under study. Moreover, codon context pattern was also seen variable in these bacteria. These results clearly indicate the variation in the codon usage pattern in these bacterial genomes.
Description: Not Available
ISSN: Not Available
Type(s) of content: Article
Sponsors: Not Available
Language: English
Name of Journal: Biochemistry & Analytical Biochemistry
NAAS Rating: Not Available
Volume No.: 5:1
Page Number: Not Available
Name of the Division/Regional Station: Centre for Agricultural Bioinformatics
Source, DOI or any other URL: doi.org/10.4172/2161-1009.1000257
URI: http://krishi.icar.gov.in/jspui/handle/123456789/34084
Appears in Collections:AEdu-IASRI-Publication

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