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. 2013 Nov 10;530(2):193-200.
doi: 10.1016/j.gene.2013.08.046. Epub 2013 Aug 25.

In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

Chaudhary Mashhood Alam  1 , Avadhesh Kumar Singh, Choudhary Sharfuddin, Safdar Ali
Affiliations

In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

Chaudhary Mashhood Alam et al. Gene. .

Abstract

An in-silico analysis of simple sequence repeats (SSRs) in 30 species of tobamoviruses was done. SSRs (mono to hexa) were present with variant frequency across species. Compound microsatellites, primarily of variant motifs accounted for up to 11.43% of the SSRs. Motif duplications were observed for A, T, AT, and ACA repeats. (AG)-(TC) was the most prevalent SSR-couple. SSRs were differentially localized in the coding region with ~54% on the 128 kDa protein while 20.37% was exclusive to 186 kDa protein. Characterization of such variations is important for elucidating the origin, sequence variations, and structure of these widely used, but incompletely understood sequences.

Keywords: CP; Coat protein; Compound simple sequence repeat; Correlation studies; IMEx; Imperfect Microsatellite Extraction; MP; Movement protein; RA; RD; Relative abundance; Relative density; SSR; Simple sequence repeat; Simple sequence repeats; Tobamovirus; cSSR; dMAX.

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