PGAP: Pan-genomes analysis pipeline

Yongbing Zhao; Jiayan Wu; Junhui Yang; Shixiang Sun; Jingfa Xiao; J. Yu

doi:10.1093/bioinformatics/btr655

PGAP: Pan-genomes analysis pipeline

Yongbing Zhao
, Jiayan Wu
, Junhui Yang
, Shixiang Sun
, Jingfa Xiao
, J. Yu

Research output: Contribution to journal › Article › peer-review

469 Scopus citations

Abstract

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.

Original language	English (US)
Article number	btr655
Pages (from-to)	416-418
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btr655
State	Published - Feb 2012
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr655

Cite this

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title = "PGAP: Pan-genomes analysis pipeline",

abstract = "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.",

author = "Yongbing Zhao and Jiayan Wu and Junhui Yang and Shixiang Sun and Jingfa Xiao and J. Yu",

note = "Funding Information: Funding: National Basic Research Program (973 Program) (No. 2010CB126604); Special Foundation Work Program (No. 2009FY120100), Ministry of Science and Technology of the People{\textquoteright}s Republic of China; National Science Foundation of China (No. 31071163).",

year = "2012",

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doi = "10.1093/bioinformatics/btr655",

language = "English (US)",

volume = "28",

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T2 - Pan-genomes analysis pipeline

AU - Zhao, Yongbing

AU - Wu, Jiayan

AU - Yang, Junhui

AU - Sun, Shixiang

AU - Xiao, Jingfa

AU - Yu, J.

N1 - Funding Information: Funding: National Basic Research Program (973 Program) (No. 2010CB126604); Special Foundation Work Program (No. 2009FY120100), Ministry of Science and Technology of the People’s Republic of China; National Science Foundation of China (No. 31071163).

PY - 2012/2

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AB - 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.

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PGAP: Pan-genomes analysis pipeline

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