Using genomic signatures for HIV-1 sub-typing.

BMC Bioinformatics
Aridaman Pandit, Somdatta Sinha

Abstract

Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of Acquired Immune Deficiency Syndrome (AIDS), exhibits very high genetic diversity with different variants or subtypes prevalent in different parts of the world. Proper classification of the HIV-1 subtypes, displaying differential infectivity, plays a major role in monitoring the epidemic and is also a critical component for effective treatment strategy. The existing methods to classify HIV-1 sequence subtypes, based on phylogenetic analysis focusing only on specific genes/regions, have shown inconsistencies as they lack the capability to analyse whole genome variations. Several isolates are left unclassified due to unresolved sub-typing. It is apparent that classification of subtypes based on complete genome sequences, rather than sub-genomic regions, is a more robust and comprehensive approach to address genome-wide heterogeneity. However, no simple methodology exists that directly computes HIV-1 subtype from the complete genome sequence. We use Chaos Game Representation (CGR) as an approach to identify the distinctive genomic signature associated with the DNA sequence organisation in different HIV-1 subtypes. We first analysed the effect of nucleotide word len...Continue Reading

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Citations

Feb 8, 2011·Archives of Virology·Takashi MatsumotoAkira Nishizono
Dec 29, 2013·Journal of Genetics·Aridaman PanditSomdatta Sinha
Jan 12, 2011·BMC Bioinformatics·Hatice Ulku Osmanbeyoglu, Madhavi K Ganapathiraju
Apr 13, 2011·BMC Bioinformatics·Thomas UnterthinerIngo Bulla
May 25, 2012·PloS One·Sanjiv K Dwivedi, Supratim Sengupta
Dec 3, 2014·Computational Biology and Chemistry·Jie TangXiaoli Xie
Oct 23, 2012·Journal of Theoretical Biology·Shuyan DingTianming Wang
Apr 10, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Yongwen LuoXiaofeng Guo
Mar 10, 2015·Journal of Theoretical Biology·Tung HoangStephen S-T Yau
Dec 14, 2011·Molecular Phylogenetics and Evolution·Aridaman PanditSomdatta Sinha
May 23, 2015·PloS One·Lila KariNikesh S Dattani
Aug 8, 2015·BMC Bioinformatics·Rallis KaramichalisSteffen Kopecki
Dec 23, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hsin-Hsiung Huang, Senthil B Girimurugan
Aug 24, 2016·BMC Bioinformatics·Rallis KaramichalisStephen Solis-Reyes
Feb 18, 2019·Statistical Applications in Genetics and Molecular Biology·Hsin-Hsiung Huang, Senthil Balaji Girimurugan

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Datasets Mentioned

BETA
AB428555
DQ207941
K03455

Software Mentioned

PHYLIP
CGR
SplitsTree4

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