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Comparative study of Codon usage pattern and compositional distribution between whole genome and virulence gene set of Vibrio cholerae N16961 | Deb | Computational Molecular Biology

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Comparative study of Codon usage pattern and compositional distribution between whole genome and virulence gene set of Vibrio cholerae N16961  

Sushanta Deb , Surajit Basak
Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, India
Author    Correspondence author
Computational Molecular Biology, 2015, Vol. 5, No. 6   doi: 10.5376/cmb.2015.05.0006
Received: 31 Aug., 2015    Accepted: 12 Oct., 2015    Published: 16 Nov., 2015
© 2015 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Deb S. and Basak S., 2015, Comparative study of Codon usage pattern and compositional distribution between whole genome and virulence gene set of <i>Vibrio cholerae</i> N16961., Computational Molecular Biology, Vol.5, No.6 1-4 (doi: 10.5376/cmb.2015.05.0006)

Abstract

Vibrio cholerae is the pathogenic organism causes cholera, a severe diarrheal disease. Occurs frequently in southern Asia. Vibrio cholerae has both pathogenic and nonpathogenic strains that vary in their virulence gene content. Great variety of strains and biotypes of Vibrio cholerae are found. These varieties are involve in shuffling of different pathogenic factors  among them such as receiving and transferring genes for toxins, colonization factors, antibiotic resistance, capsular polysaccharides which giving  resistance to chlorine 7 and new surface antigens, such as the 0139 lip polysaccharide and O antigen capsule. Different mode of transfer of these virulence gene i.e. lateral and horizontal transfer by phase, collection of pathogenic genes and other accessory genetic element, pave the way to understand how bacterial pathogen develop its Pathogenicity and become a new strain. To provide a insights into the genetic features and the relationship between the overall codon usage pattern of virulence gene set (VGS).We measure the GC content of VGS which shows that there is no any difference between GC content of whole genome and VGS .It also has been found that GC content shows the similar distribution among the CDS of both whole genome and Virulence gene set. A correlation analysis between the A3s, T3s, G3s, C3s, and GC3s, the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC %) indicated that mutational bias plays role in shaping the VGS codon usage bias.

Keywords
Codon usage pattern; whole genome; virulence gene; Vibrio cholera
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