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Bioinformatics. 2014 May 1;30(9):1297-9. doi: 10.1093/bioinformatics/btu017. Epub 2014 Jan 13.

PanGP: a tool for quickly analyzing bacterial pan-genome profile.

Author information

1
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

Abstract

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.

PMID:
24420766
PMCID:
PMC3998138
DOI:
10.1093/bioinformatics/btu017
[Indexed for MEDLINE]
Free PMC Article

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