Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
Gene. 2013 Apr 10;518(1):114-23. doi: 10.1016/j.gene.2012.11.063. Epub 2013 Jan 12.
Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project.
由于微生物具有携带抗生素和致病活性的能力，因此对微生物基因组进行测序非常重要。然而，即使有新的组装软件的帮助，完成整个基因组仍然是一项耗时的任务。在大多数细菌中，致病或抗生素基因都存在于基因组岛中。因此，快速的基因组岛（GI）预测方法对于正在进行的测序基因组非常有用。在这项工作中，我们构建了一个名为 GI-POP（http://gipop.life.nthu.edu.tw）的 Web 服务器，它集成了序列组装工具、功能注释管道和基于支持向量机（SVM）的基因组岛基因组特征扫描（GI-GPS）高绩效 GI 预测模块。正在进行的基因组项目的草图基因组可以提交到我们的 Web 服务器，它提供功能注释和高度可能的 GI 预测结果。GI-POP 是一个全面的注释 Web 服务器，专为正在进行的基因组项目分析而设计。研究人员可以从他们的草图基因组中执行注释并获得预分析信息，包括可能的 GI、编码/非编码序列和功能分析。这个预分析系统可以为完成基因组测序项目提供有用的信息。
