An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics, 21(19): 3797-800 (2005).

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Title: An automated genotyping system for analysis of HIV-1 and other microbial sequences
Authors: de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R, Vandamme AM.
Journal: Bioinformatics,21(19):3797-800 (2005)

Journal Impact Factor (I.F.): 5.468
Number of citations (Google Scholar): 435

Abstract

MOTIVATION: Genetic analysis of HIV-1 is important not only for vaccine development, but also to guide treatment strategies, track the emergence of new viral variants and ensure that diagnostic assays are contemporary and fully optimized. However, most genotyping methods are laborious and complex, and involve the use of multiple software applications. Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens.

RESULTS: The new REGA subtyping tool, developed using Java programming and PERL scripts, combines phylogenetic analyses with boot-scanning methods for the genetic subtyping of full-length and subgenomic fragments of HIV-1. When used to investigate the subtype of previously published reference datasets that were analysed using manual phylogenetic methods, the automated method correctly identified 97.5-100% of non-recombinant and circulating recombinant forms of HIV-1, including 108 full-length, 108 gag and 221 env sequences downloaded from the Los Alamos database

Download: Full text paper

Citation: de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R, Vandamme AM. An automated genotyping system for analysis of HIV-1 and other microbial sequences Bioinformatics,21(19):3797-800 (2005).


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KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

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