title: An automated genotyping system for analysis of HIV-1 and other microbial sequences.
abstract: BACKGROUND
  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.
authors.affiliation: Evolution Group at the Zoology Department, University of Oxford, UK. tulio.deoliveira@zoology.oxford.ac.uk
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
authors.forename: Koen
authors.initials: K
authors.lastname: Deforche
authors.forename: Sharon
authors.initials: S
authors.lastname: Cassol
authors.forename: Mika
authors.initials: M
authors.lastname: Salminen
authors.forename: Dimitris
authors.initials: D
authors.lastname: Paraskevis
authors.forename: Chris
authors.initials: C
authors.lastname: Seebregts
authors.forename: Joe
authors.initials: J
authors.lastname: Snoeck
authors.forename: Estrelita Janse
authors.initials: EJ
authors.lastname: van Rensburg
authors.forename: Annemarie M J
authors.initials: AM
authors.lastname: Wensing
authors.forename: David A
authors.initials: DA
authors.lastname: van de Vijver
authors.forename: Charles A
authors.initials: CA
authors.lastname: Boucher
authors.forename: Ricardo
authors.initials: R
authors.lastname: Camacho
authors.forename: Anne-Mieke
authors.initials: AM
authors.lastname: Vandamme
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004279:DNA, Viral / Q000032:analysis / Q000235:genetics*; D005838:Genotype; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004279:DNA, Viral