کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5920510 | 1164291 | 2012 | 8 صفحه PDF | دانلود رایگان |

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.
Highlights⺠Multifractal dimension can be used to classify retroviral genomes. ⺠Closely related genomes (HIV-1 subtypes) cannot be resolved using dimension alone. ⺠Combination of multifractal measures is required to resolve HIV-1 subtypes. ⺠Multifractal measure based clustering match phylogenetic relationships. ⺠The method is simple and faster than conventional alignment-based methods.
Journal: Molecular Phylogenetics and Evolution - Volume 62, Issue 2, February 2012, Pages 756-763