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In-Silico Analysis of SSR and cSSR in Flavivirus

At present we are working on In-Silico analysis of SSR and cSSR present in genera of L5-likevirus and Flavivirus. In-Silico analysis refers the computational analysis in the field of biology. We use In-Silico analysis to find the simple sequence repeats (SSR) and compound simple sequence repeats (cSSR) in genome.After finding the simple sequence repeats present in genomes of different family of viruses we hypothesize the role of these repeat sequences in there function. Simple sequence repeats (SSRs), also called as microsatellites and minisatellites are tandem repetitions of relatively short motifs of DNA.Simple microsatellites are ubiquitous in eukaryotic and prokaryotic genomes but relatively rare in viruses with smaller genomes such as Human Immunodeficiency Virus Type 1 (HIV-1). Variable length of microsatellites may affect local DNA structure or the encoded proteins. Role of such sequences in gene regulation, transcription and protein function has been elucidated in few cases However, microsatellites with interruptions between the repeats are also known, which are classified as interrupted pure, compound, interrupted compound, complex and interrupted complex. Compound microsatellites are composed of two or more microsatellites residing directly adjacent to each other. These have been found in diverse taxa including viruses, prokaryotes and eukaryotes. Although microsatellites have attracted a lot of attention with respect to their origin, distribution, roles and evolution, the presence and possible functional significance of SSRs in plant viruses have been recognized very recently. Because of high polymorphisms, microsatellites have been used widely as markers to study population genetic in humans and linkage association in crop plants such as cotton. Similarly due to their high mutability, microsatellites are thought to play a significant role in genome evolution by creating and maintaining quantitative genetic variation. Microsatellites are present with varying frequency across genomes in both coding and non-coding regions. It has been suggested that this difference arises from increased selection in coding regions. Interestingly, microsatellites are more abundant in coding regions than in noncoding regions in eukaryotes and some prokaryotes. In viruses, microsatellites are mostly accumulated in the coding regions probably due to high coding density of viral genome. Thus non-random distribution, high polymorphisms and diversity are characteristic features of all microsatellite sequences analyzed so far.

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