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

被引：30

作者：

Myers, RE

Gale, CV

Harrison, A

Takeuchi, Y

Kellam, P ^{[1
]}

机构：

[1] Univ Coll, Dept Infect, London, England

[2] Univ Coll, Dept Immunol & Mol Pathol, London, England

[3] Univ Coll, Dept Biochem, London, England

来源：

BIOINFORMATICS | 2005年 / 21卷 / 17期

基金：

英国医学研究理事会;

关键词：

D O I：

10.1093/bioinformatics/bti569

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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%.

引用

页码：3535 / 3540

页数：6

共 18 条

[1] Evidence and consequence of porcine endogenous retrovirus recombination [J].