Multifractal analysis of HIV-1 genomes

Pandit, Aridaman ; Dasanna, Anil Kumar ; Sinha, Somdatta (2012) Multifractal analysis of HIV-1 genomes Molecular Phylogenetics and Evolution, 62 (2). pp. 756-763. ISSN 1055-7903

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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.

Item Type:Article
Source:Copyright of this article belongs to Elsevier Science.
Keywords:Multifractal Analysis; Alignment-Free Method; Retrovirus; HIV-1 Subtypes; Phylogenetic Analysis
ID Code:92958
Deposited On:08 Jun 2012 10:27
Last Modified:08 Jun 2012 10:38

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