Wu Xiaomeng, Cai Zhipeng, Wan Xiu-Feng, Hoang Tin, Goebel Randy, Lin Guohui
Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
Bioinformatics. 2007 Jul 15;23(14):1744-52. doi: 10.1093/bioinformatics/btm248. Epub 2007 May 11.
The availability of the whole genomic sequences of HIV-1 viruses provides an excellent resource for studying the HIV-1 phylogenies using all the genetic materials. However, such huge volumes of data create computational challenges in both memory consumption and CPU usage.
We propose the complete composition vector representation for an HIV-1 strain, and a string scoring method to extract the nucleotide composition strings that contain the richest evolutionary information for phylogenetic analysis. In this way, a large-scale whole genome phylogenetic analysis for thousands of strains can be done both efficiently and effectively. By using 42 carefully curated strains as references, we apply our method to subtype 1156 HIV-1 strains (10.5 million nucleotides in total), which include 825 pure subtype strains and 331 recombinants. Our results show that our nucleotide composition string selection scheme is computationally efficient, and is able to define both pure subtypes and recombinant forms for HIV-1 strains using the 5000 top ranked nucleotide strings.
The Java executable and the HIV-1 datasets are accessible through 'http://www.cs.ualberta.ca/~ghlin/src/WebTools/hiv.php.
Supplementary data are available at Bioinformatics online.
HIV-1病毒全基因组序列的可得性为利用所有遗传物质研究HIV-1系统发育提供了极好的资源。然而，如此大量的数据在内存消耗和CPU使用方面都带来了计算挑战。
我们提出了一种针对HIV-1毒株的完整组成向量表示法，以及一种字符串评分方法，以提取包含用于系统发育分析的最丰富进化信息的核苷酸组成字符串。通过这种方式，可以高效且有效地对数千个毒株进行大规模全基因组系统发育分析。我们以42个经过精心挑选的毒株作为参考，将我们的方法应用于1156个HIV-1毒株（总共1050万个核苷酸），其中包括825个纯亚型毒株和331个重组毒株。我们的结果表明，我们的核苷酸组成字符串选择方案在计算上是高效的，并且能够使用排名前5000的核苷酸字符串来定义HIV-1毒株的纯亚型和重组形式。
Java可执行文件和HIV-1数据集可通过“http://www.cs.ualberta.ca/~ghlin/src/WebTools/hiv.php”获取。
补充数据可在《生物信息学》在线获取。
