Zhang Ming, Schultz Anne-Kathrin, Calef Charles, Kuiken Carla, Leitner Thomas, Korber Bette, Morgenstern Burkhard, Stanke Mario
Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W463-5. doi: 10.1093/nar/gkl255.
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al. The input data for our server is a partial or complete genome sequence from HIV-1; our tool assigns regions of the input sequence to known subtypes of HIV-1 and predicts phylogenetic breakpoints. jpHMM is available online at http://jphmm.gobics.de/.
检测人类免疫缺陷病毒（HIV-1）基因组序列中的重组对于流行病学研究和疫苗开发至关重要。在此，我们展示了一个用于HIV-1系统发育断点亚型分析和定位的网络服务器。我们的软件基于跳跃轮廓隐马尔可夫模型（jpHMM），它是Spang等人提出的跳跃比对方法的概率推广。我们服务器的输入数据是HIV-1的部分或完整基因组序列；我们的工具将输入序列的区域分配给HIV-1的已知亚型，并预测系统发育断点。jpHMM可在http://jphmm.gobics.de/在线获取。
