title: In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes.
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.
authors: Department of Botany, Patna University, Bihar 800005, India.
authors: Chaudhary Mashhood
authors: CM
authors: Alam
authors: Avadhesh Kumar
authors: AK
authors: Singh
authors: Choudhary
authors: C
authors: Sharfuddin
authors: Safdar
authors: S
authors: Ali
mesh_terms: D002874:Chromosome Mapping; D003198:Computer Simulation; D016679:Genome, Viral; D018895:Microsatellite Repeats; D008957:Models, Genetic; D016366:Open Reading Frames; D010935:Plant Diseases / Q000821:virology; D017898:Tobamovirus / Q000235:genetics* / Q000378:metabolism
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