A Brief Review of Software Tools for Pangenomics

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific pub...

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Bibliographic Details
Published in:Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2015-02, Vol.13 (1), p.73-76
Main Authors: Xiao, Jingfa, Zhang, Zhewen, Wu, Jiayan, Yu, Jun
Format: Article
Language:English
Subjects:
Comparative analysis
Core genes
Genomic dynamics
Pangenome
Pangenomics
Resource Review
原核生物
同源基因
基因组分析
生物信息学
系统发育
结构元素
软件工具
非编码RNA
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Summary:Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
ISSN:1672-0229
2210-3244
DOI:10.1016/j.gpb.2015.01.007