Title: An automated genotyping system for analysis of HIV-1 and other microbial sequences
Authors: de Oliveira, Tulio ×
Deforche, Koen
Cassol, Sharon
Salminen, Mika
Paraskevis, Dimitris
Seebregts, Chris
Snoeck, Joke
van Rensburg, Estrelita Janse
Wensing, Annemarie M J
van de Vijver, David A
Boucher, Charles A
Camacho, Ricardo
Vandamme, Anne-Mieke #
Issue Date: Oct-2005
Publisher: Oxford University Press
Series Title: Bioinformatics vol:21 issue:19 pages:3797-3800
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.
ISSN: 1367-4803
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
× corresponding author
# (joint) last author

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