PanGP: A tool for quickly analyzing bacterial pan-genome profile

Pan-genome analyses have shed light on the dynamics and evolution of bacterial genome from the point of population. The explosive growth of bacterial genome sequence also brought an extremely big challenge to pan-genome profile analysis. We developed a tool, named PanGP, to complete pan-genome profi...

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Bibliographic Details
Published in:Bioinformatics 2014-05, Vol.30 (9), p.1297-1299
Main Authors: Zhao, Yongbing, Jia, Xinmiao, Yang, Junhui, Ling, Yunchao, Zhang, Zhang, Yu, Jun, Wu, Jiayan, Xiao, Jingfa
Format: Article
Language:English
Subjects:
Algorithms
Applications Notes
Bacteria
Bacteria - genetics
Bioinformatics
Dynamic tests
Evolution
Genome, Bacterial
Genomes
Genomics - methods
High-Throughput Nucleotide Sequencing - methods
Multigene Family
Software
Strain
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Summary:Pan-genome analyses have shed light on the dynamics and evolution of bacterial genome from the point of population. The explosive growth of bacterial genome sequence also brought an extremely big challenge to pan-genome profile analysis. We developed a tool, named PanGP, to complete pan-genome profile analysis for large-scale strains efficiently. PanGP has integrated two sampling algorithms, totally random (TR) and distance guide (DG). The DG algorithm drew sample strain combinations on the basis of genome diversity of bacterial population. The performance of these two algorithms have been evaluated on four bacteria populations with strain numbers varying from 30 to 200, and the DG algorithm exhibited overwhelming advantage on accuracy and stability than the TR algorithm. Availability: PanGP was developed with a user-friendly graphic interface and it was available at http://PanGP.big.ac.cn. Contact: xiaojingfa@big.ac.cn or wujy@big.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btu017