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Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. eCollection 2018.

PGAweb: A Web Server for Bacterial Pan-Genome Analysis.

Chen X1, Zhang Y2,3,4, Zhang Z2,3, Zhao Y5, Sun C6, Yang M7, Wang J2,3,4, Liu Q1,8, Zhang B1,8, Chen M2,3, Yu J3,4, Wu J3, Jin Z1,8, Xiao J2,3,4.

Author information

1
Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
2
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
3
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
4
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
5
Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States.
6
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, United States.
7
Office of General Affairs, Chinese Academy of Sciences, Beijing, China.
8
Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China.

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:

bacterial pan-genome analysis; genome dynamics visualization; genome structure interpretation; orthologous gene identification; web server

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