An automated genotyping system for analysis of HIV-1 and other microbial sequences

• Published in: Bioinformatics 2005-10, Vol.21 (19), p.3797-3800
• Main Authors: de Oliveira, Tulio, Deforche, Koen, Cassol, Sharon, Salminen, Mika, Paraskevis, Dimitris, Seebregts, Chris, Snoeck, Joe, van Rensburg, Estrelita Janse, Wensing, Annemarie M. J., van de Vijver, David A., Boucher, Charles A., Camacho, Ricardo, Vandamme, Anne-Mieke
• Format: Article
• Language: English
• Subjects: Algorithms; Artificial Intelligence; Base Sequence; Biological and medical sciences; Chromosome Mapping - methods; DNA, Viral - analysis; DNA, Viral - genetics; Fundamental and applied biological sciences. Psychology; General aspects; Genotype; HIV-1 - genetics; Human immunodeficiency virus 1; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Pattern Recognition, Automated - methods; Phylogeny; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti607

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. Availability: The tool, which can be easily downloaded and installed on either a UNIX or Linux-based computer system, is available at http://www.bioafrica.net/subtypetool/html/ Contact: [e-mail]