Distributional analysis and motif frequencies of compound microsatellite repeats in viral genomes

Abstract

Viruses are very small organisms that incorporate their DNA into host cells and cause several diseases. They evolve extremely faster when compared to other organisms. Viruses can develop into new strains easily due to their shorter generation times and due to rapid changes in their genome sequences (in the form of mutations) during the course of evolution. In view of the recent pandemics of viruses such as HIV, SARS, Swine flu, Huntavirus, etc., studying the evolution of viruses at genomic level would be very informative. A special type of DNA repeats named compound microsatellites are often studied to understand the genomic evolution of organisms. This paper presents the details of the study performed to analyze the distribution of compound microsatellites and their motif preferences in all sequenced viral genomes using the classical data mining algorithm called Apriori Algorithm. It is interesting to note that the dynamics of compound microsatellites in viruses differ from that of higher organisms. We observed that viral compound microsatellites are not composed of similar or identical motifs unlike humans and other higher organisms where more than 90% of them are composed of similar motifs. © 2012 IEEE.