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Bioinformatics Advance Access published online on July 26, 2005
Bioinformatics, 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@oupjournals.org
Received March 23, 2005
Revised June 23, 2005
Accepted June 30, 2005

Article

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

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


  Abstract

Motivation: HIV-1 anti-retroviral 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) (Gale et al. 2004) 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. 98% of the 141 sequences used to define the subtype alignments 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.


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