Introduction

SUMMARY: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains. AVAILABILITY: PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net. CONTACT: junyu@big.ac.cn; xiaojingfa@big.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. PGAP: pan-genomes analysis pipeline.
    Cite this
    Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J, 2012-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Yongbing Zhao
    Developer

  2. Jiayan Wu
    Developer

  3. Junhui Yang
    Developer

  4. Shixiang Sun
    Developer

  5. Jingfa Xiao
    Developer

  6. Jun Yu
    Investigator

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Summary
AccessionBT006813
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByJun Yu