title: Multifractal analysis of HIV-1 genomes.
abstract: Pathogens like HIV-1, which evolve into many closely related variants displaying differential infectivity and evolutionary dynamics in a short time scale, require fast and accurate classification. Conventional whole genome sequence alignment-based methods are computationally expensive and involve complex analysis. Alignment-free methodologies are increasingly being used to effectively differentiate genomic variations between viral species. Multifractal analysis, which explores the self-similar nature of genomes, is an alignment-free methodology that has been applied to study such variations. However, whether multifractal analysis can quantify variations between closely related genomes, such as the HIV-1 subtypes, is an open question. Here we address the above by implementing the multifractal analysis on four retroviral genomes (HIV-1, HIV-2, SIVcpz, and HTLV-1), and demonstrate that individual multifractal properties can differentiate between different retrovirus types easily. However, the individual multifractal measures do not resolve within-group variations for different known subtypes of HIV-1 M group. We show here that these known subtypes can instead be classified correctly using a combination of the crucial multifractal measures. This method is simple and computationally fast in comparison to the conventional alignment-based methods for whole genome phylogenetic analysis.
authors.affiliation: Mathematical Modeling and Computational Biology Group, Centre for Cellular and Molecular Biology (CSIR), Hyderabad 500007, India.
authors.forename: Aridaman
authors.initials: A
authors.lastname: Pandit
authors.forename: Anil Kumar
authors.initials: AK
authors.lastname: Dasanna
authors.forename: Somdatta
authors.initials: S
authors.lastname: Sinha
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D014644:Genetic Variation; D020745:Genome, Archaeal; D016679:Genome, Viral; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D015498:HIV-2 / Q000145:classification / Q000235:genetics*; D015368:Human T-lymphotropic virus 1 / Q000235:genetics*; D006801:Humans; D008962:Models, Theoretical; D005810:Multigene Family; D015999:Multivariate Analysis; D010802:Phylogeny; D025341:Principal Component Analysis; D015302:Simian Immunodeficiency Virus / Q000235:genetics*; D013045:Species Specificity