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


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


BACKGROUND
p.kellam@ucl.ac.uk


BACKGROUND
http://pgv19.virol.ucl.ac.uk/download/star_supplement
Myers
R E
RE
Department of Immunology and Molecular Pathology, University College London, UK.
Gale
C V
CV
Harrison
A
A
Takeuchi
Y
Y
Kellam
P
P
D000465:Algorithms; D000595:Amino Acid Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016333:HIV Protease / Q000032:analysis / Q000737:chemistry* / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D016333:HIV Protease