In silico survey of distribution and frequency of imperfect microsatellite repeats in viral genomes

Abstract

Microsatellites are short, dynamic tandem repeats in DNA sequences that are unique in nature and are widely used in several fields including DNA Fingerprinting, Paternity Studies, Forensics, Population Studies and Evolutionary studies. This paper presents the first comprehensive computational study of microsatellite repeats in viruses. Microsatellites from more than 3,500 viral sequences have been analyzed to underpin the genomic differences in them, their variation in terms of size and genes, distribution of microsatellite repeats based on their motif-size, location and also the motif preferences of such microsatellite repeats in all these sequences. The study revealed that the viral genomes differ a lot in terms of their genome composition and also in terms of the microsatellite distribution. We found that the majority of microsatellites are in the coding regions suggesting selection towards pathogen adaptation and faster evolution. It is also observed that viruses are selective in nature to form microsatellites with certain motifs only. © 2012 IEEE.