Journal
FRONTIERS IN MICROBIOLOGY
Volume 9, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2018.01910
Keywords
web server; bacterial pan-genome analysis; genome dynamics visualization; genome structure interpretation; orthologous gene identification
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Funding
- National Natural Science Foundation of China [31771465, 31471248, 31501024]
- National Key Research Program of China [2016YFB0201701, 2016YFB0201702, 2017YFC0907503]
- National Development and Reform Commission of China [2016-999999-65-01-000696-07]
- Chinese Academy of Sciences [KJZD-EW-L14]
- 13th Five-Year Informatization Plan of Chinese Academy of Sciences [XXH13503-05]
- Youth Innovation Promotion Association of CAS
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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/.
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