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Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29.

PGAP: pan-genomes analysis pipeline.

Author information

1
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China.

Abstract

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.

PMID:
22130594
PMCID:
PMC3268234
DOI:
10.1093/bioinformatics/btr655
[Indexed for MEDLINE]
Free PMC Article

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