alexa Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus
ISSN: 2153-0602

Journal of Data Mining in Genomics & Proteomics
Open Access

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Research Article

Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus

Chaudhary Mashhhood Alam1,2, Asif Iqbal1, Babita Thadari2 and Safdar Ali2*

1PIRO Technologies Private Limited, New Delhi-110025, India

2Department of Biomedical Sciences, SRCASW, University of Delhi, Vasundhara Enclave, New Delhi-110096, India

*Corresponding Author:
Safdar Ali
Assistant Professor
Department of Biomedical Sciences
SRCASW, University of Delhi, New Delhi – 110096, India
Tel: 91-11-22623503
Fax: 91-11-22623504
E-mail: [email protected]; [email protected]

Received date: January 21, 2016 Accepted date: January 28, 2016 Published date: February 06, 2016

Citation: Alam CM, Iqbal A, Thadari B, Ali S (2016) Imex Based Analysis of Repeat Sequences in Flavivirus Genomes, Including Dengue Virus. J Data Mining Genomics Proteomics 7:187. doi:10.4172/2153-0602.1000187

Copyright: © 2016 Alam CM, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

Simple sequence repeats (SSRs), also known as microsatellites, are 1-6 nucleotides repeat motif, present in varying number of iterations, across coding and non-coding regions of prokaryotes, eukaryotes and viruses. Present study focuses on simple sequence repeats (SSRs) in 27 Flavivirus genomes, which includes dengue virus. The comparative viral genomics in the light of SSRs would help us understand the diversity and adaptability to new hosts. A total of 1164 SSRs and 53 cSSRs were uncovered from the 27studied genomes. Mononucleotide A was the most prevalent repeat motif with an average distribution of around 6. This was followed by G (average distribution of 2). Amongst the dinucleotides AG/GA repeat motif was the most prevalent with an average distribution of 14 across studied genomes. The Flavivirus genomes lacked two essential features responsible for genome evolution, dinucleotide repeat motif AT/TA (least represented with average distribution of ~0.5) and cSSR in non-coding regions, suggesting a stable genome or evolution by hitherto unexplained mechanisms. The unveiling of conserved sequences in the isolates of Dengue virus suggests a basis for biomarker development for viral diagnostics.

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