Chen Xinyu, Zhang Yadong, Zhang Zhewen, Zhao Yongbing, Sun Chen, Yang Ming, Wang Jinyue, Liu Qian, Zhang Baohua, Chen Meili, Yu Jun, Wu Jiayan, Jin Zhong, Xiao Jingfa
Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. eCollection 2018.
An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool for bacterial pan-genome analysis, which is composed of two main pan-genome analysis modules, PGAP and PGAP-X. PGAweb provides key interactive and customizable functions that include orthologous clustering, pan-genome profiling, sequence variation and evolution analysis, and functional classification. PGAweb presents features of genomic structural dynamics and sequence diversity with different visualization methods that are helpful for intuitively understanding the dynamics and evolution of bacterial genomes. PGAweb has an intuitive interface with one-click setting of parameters and is freely available at http://PGAweb.vlcc.cn/.
近年来，微生物基因组数据呈天文数字增长，这导致对用于物种内和跨物种泛基因组分析的生物信息学工具的需求强劲。在此，我们展示了PGAweb，这是一个用户友好的基于网络的细菌泛基因组分析工具，它由两个主要的泛基因组分析模块PGAP和PGAP-X组成。PGAweb提供了关键的交互式和可定制功能，包括直系同源聚类、泛基因组分析、序列变异和进化分析以及功能分类。PGAweb通过不同的可视化方法展示基因组结构动态和序列多样性的特征，这有助于直观地理解细菌基因组的动态和进化。PGAweb具有直观的界面，可一键设置参数，可在http://PGAweb.vlcc.cn/免费获取。
