PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 09 2022
15 09 2022
Historique:
received:
26
11
2021
revised:
09
07
2022
accepted:
29
07
2022
pubmed:
3
8
2022
medline:
15
11
2022
entrez:
2
8
2022
Statut:
ppublish
Résumé
As pan-genome approaches are largely employed for bacterial comparative genomics and evolution analyses, but still difficult to be carried out by non-bioinformatician biologists, there is a need for an innovative tool facilitating the exploration of bacterial pan-genomes. PanExplorer is a web application providing various genomic analyses and reports, giving intuitive views that enable a better understanding of bacterial pan-genomes. As an example, we produced the pan-genome for 121 Anaplasmataceae strains (including 30 Ehrlichia, 15 Anaplasma, 68 Wolbachia). PanExplorer is written in Perl CGI and relies on several JavaScript libraries for visualization (hotmap.js, MauveViewer, CircosJS). It is freely available at http://panexplorer.southgreen.fr. The source code has been released in a GitHub repository https://github.com/SouthGreenPlatform/PanExplorer. A documentation section is available on PanExplorer website.
Identifiants
pubmed: 35916725
pii: 6653297
doi: 10.1093/bioinformatics/btac504
pmc: PMC9477528
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4412-4414Subventions
Organisme : European Union on the Guadeloupe Region
Organisme : European Research and Development Funds
ID : 2018-FED-1084
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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