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Frontiers in microbiology
2018;9 1910.

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

Xinyu Chen, Yadong Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun, Ming Yang, Jinyue Wang, Qian Liu, Baohua Zhang, Meili Chen, Jun Yu, Jiayan Wu, Zhong Jin, Jingfa Xiao
Author Information
  1. Xinyu Chen: Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
  2. Yadong Zhang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  3. Zhewen Zhang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  4. Yongbing Zhao: Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States.
  5. Chen Sun: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, United States.
  6. Ming Yang: Office of General Affairs, Chinese Academy of Sciences, Beijing, China.
  7. Jinyue Wang: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  8. Qian Liu: Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
  9. Baohua Zhang: Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
  10. Meili Chen: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  11. Jun Yu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  12. Jiayan Wu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  13. Zhong Jin: Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.
  14. Jingfa Xiao: BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
PMID: 30186253 DOI: 10.3389/fmicb.2018.01910

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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