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Bioinformatics Advance Access originally published online on July 26, 2005
Bioinformatics 2005 21(17):3535-3540; doi:10.1093/bioinformatics/bti569
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)

R. E. Myers 1, C. V. Gale 2, A. Harrison 3, Y. Takeuchi 1 and P. Kellam 2,*

1Department of Immunology and Molecular Pathology, University College London
2Department of Infection, University College London
3Department of Biochemistry, University College London

*To whom correspondence should be addressed.

Motivation: HIV-1 antiretroviral drug resistance testing produces large amounts of HIV-1 protease and reverse transcriptase sequences. These provide an excellent resource to study the incidence, spread and clinical significance of HIV-1 subtypes. We have produced a program, Subtype Analyser (STAR) that rapidly and accurately subtypes HIV-1. Here we have determined a robust and statistically validated model for subtype assignment.

Results: We have significantly extended our HIV-1 subtyping tool (STAR), such that each query sequence when evaluated against subtype profile alignments, returns a discriminating score based on the ratio of subtype positive to negative amino acid positions. These scores were transformed into a Z-score distribution and evaluated. Of the 141 sequences used to define the subtype alignments, 98% were correctly reclassified. Inclusion of additional recombination detection within STAR increased the detection of known recombinant sequences to 95%.

Availability: STAR is available as compiled (Linux Fedora 3) or source code from http://pgv19.virol.ucl.ac.uk/download/star_linux.tar

Contact: p.kellam{at}ucl.ac.uk

Supplementay Information: http://pgv19.virol.ucl.ac.uk/download/star_supplement

Received on March 23, 2005; revised on June 23, 2005; accepted on June 30, 2005

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