Frontiers in Microbiology (Aug 2018)
PGAweb: A Web Server for Bacterial Pan-Genome Analysis
- Xinyu Chen,
- Yadong Zhang,
- Yadong Zhang,
- Yadong Zhang,
- Zhewen Zhang,
- Zhewen Zhang,
- Yongbing Zhao,
- Chen Sun,
- Ming Yang,
- Jinyue Wang,
- Jinyue Wang,
- Jinyue Wang,
- Qian Liu,
- Qian Liu,
- Baohua Zhang,
- Baohua Zhang,
- Meili Chen,
- Meili Chen,
- Jun Yu,
- Jun Yu,
- Jiayan Wu,
- Zhong Jin,
- Zhong Jin,
- Jingfa Xiao,
- Jingfa Xiao,
- Jingfa Xiao
Affiliations
- Xinyu Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- Yadong Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Yadong Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Yadong Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Zhewen Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Zhewen Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Yongbing Zhao
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
- Chen Sun
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, United States
- Ming Yang
- Office of General Affairs, Chinese Academy of Sciences, Beijing, China
- Jinyue Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jinyue Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jinyue Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Qian Liu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- Qian Liu
- Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
- Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- Baohua Zhang
- Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
- Meili Chen
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Meili Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jun Yu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- Zhong Jin
- Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
- Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Jingfa Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- DOI
- https://doi.org/10.3389/fmicb.2018.01910
- Journal volume & issue
-
Vol. 9
Abstract
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/.
Keywords
- web server
- bacterial pan-genome analysis
- genome dynamics visualization
- genome structure interpretation
- orthologous gene identification
