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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
An automated genotyping system for analysis of HIV-1 and other microbial sequences
Bioinformatics, Volume 21, No. 19, Year 2005
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Description
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 bootscanning 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. © The Author 2005. Published by Oxford University Press. All rights reserved.
Authors & Co-Authors
De Oliveira, Tulio
United Kingdom, Oxford
University of Oxford
Deforche, Koen
Belgium, Leuven
Rega Institute for Medical Research
Cassol, Sharon A.
South Africa, Pretoria
University of Pretoria
Salminen, Mika O.
Finland, Helsinki
Terveyden ja Hyvinvoinnin Laitos
Paraskevis, D. N.
Belgium, Leuven
Rega Institute for Medical Research
Seebregts, Christopher John
South Africa, Tygerberg
South African Medical Research Council
Snoeck, Joke
Belgium, Leuven
Rega Institute for Medical Research
van Rensburg, Estrelita Janse
Netherlands, Utrecht
University Medical Center Utrecht
Wensing, Annemarie Marie J.
Netherlands, Utrecht
University Medical Center Utrecht
Van De Vijver, D. A.M.C.
Netherlands, Utrecht
University Medical Center Utrecht
Boucher, Charles A.B.
Netherlands, Utrecht
University Medical Center Utrecht
Camacho, Ricardo Jorge
Portugal, Lisbon
Centro Hospitalar de Lisboa Ocidental Hospital de Egas Moniz
Vandamme, Anne Mieke
Belgium, Leuven
Rega Institute for Medical Research
Statistics
Citations: 519
Authors: 13
Affiliations: 7
Identifiers
Doi:
10.1093/bioinformatics/bti607
ISSN:
13674803
e-ISSN:
13674811
Research Areas
Genetics And Genomics
Infectious Diseases