A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)
A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)
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DOI：
10.1093/bioinformatics/bti569
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发表时间：
2005-09-01
期刊：
影响因子：
5.8
通讯作者：
Kellam, P
中科院分区：
文献类型：
--
作者：
Myers, RE;Gale, CV;Kellam, P
动机：HIV-1抗逆转录病毒药物耐药性测试产生大量的HIV-1蛋白酶和逆转录酶序列。这些为研究HIV-1亚型的发病率、传播和临床意义提供了极好的资源。我们已经开发了一个程序，亚型分析仪（星星），可以快速准确地对HIV-1进行亚型分析。在这里，我们已经确定了一个强大的和统计学验证的模型亚型assignment.Results：我们已经显着扩展了我们的HIV-1亚型分型工具（星星），使每个查询序列时，对亚型配置文件比对评估，返回一个判别分数的基础上亚型阳性到阴性的氨基酸位置的比例。将这些分数转换为Z分数分布并进行评价。在用于定义亚型比对的141个序列中，98%被正确地重新分类。在星星中加入额外的重组检测，将已知重组序列的检出率提高至95%。
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%.