panX: pan-genome analysis and exploration

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
Autoren
  • Wei Ding
  • Franz Baumdicker
  • Richard A Neher
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000423811200005&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/nar/gkx977
eISSN
1362-4962
Externe Identifier
  • Clarivate Analytics Document Solution ID: FU4GJ
  • PubMed Identifier: 29077859
ISSN
0305-1048
Ausgabe der Veröffentlichung
1
Zeitschrift
NUCLEIC ACIDS RESEARCH
Artikelnummer
ARTN e5
Datum der Veröffentlichung
2018
Status
Published
Titel
panX: pan-genome analysis and exploration
Sub types
  • Article
Ausgabe der Zeitschrift
46

Datenquelle: Web of Science (Lite)

Andere Metadatenquellen:
Autoren
  • Wei Ding
  • Franz Baumdicker
  • Richard A Neher
DOI
10.1093/nar/gkx977
eISSN
1362-4962
ISSN
0305-1048
Ausgabe der Veröffentlichung
1
Zeitschrift
Nucleic Acids Research
Sprache
en
Online publication date
2017
Paginierung
e5 - e5
Datum der Veröffentlichung
2018
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/nar/gkx977
Datum der Datenerfassung
2019
Titel
panX: pan-genome analysis and exploration
Ausgabe der Zeitschrift
46

Datenquelle: Crossref

Abstract
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.
Addresses
  • Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Autoren
  • Wei Ding
  • Franz Baumdicker
  • Richard A Neher
DOI
10.1093/nar/gkx977
eISSN
1362-4962
Externe Identifier
  • PubMed Identifier: 29077859
  • PubMed Central ID: PMC5758898
Open access
true
ISSN
0305-1048
Ausgabe der Veröffentlichung
1
Zeitschrift
Nucleic acids research
Schlüsselwörter
  • Bacteria
  • Reproducibility of Results
  • Computational Biology
  • Genomics
  • Evolution, Molecular
  • Phylogeny
  • Genome, Bacterial
  • Multigene Family
  • Algorithms
  • Software
Sprache
eng
Medium
Print
Open access status
Open Access
Paginierung
e5
Datum der Veröffentlichung
2018
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2017
Titel
panX: pan-genome analysis and exploration.
Sub types
  • Research Support, Non-U.S. Gov't
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
46

Files

https://academic.oup.com/nar/article-pdf/46/1/e5/23327157/gkx977.pdf https://europepmc.org/articles/PMC5758898?pdf=render

Datenquelle: Europe PubMed Central

Abstract
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.
Date of acceptance
2017
Autoren
  • Wei Ding
  • Franz Baumdicker
  • Richard A Neher
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/29077859
DOI
10.1093/nar/gkx977
eISSN
1362-4962
Externe Identifier
  • PubMed Central ID: PMC5758898
Ausgabe der Veröffentlichung
1
Zeitschrift
Nucleic Acids Res
Schlüsselwörter
  • Algorithms
  • Bacteria
  • Computational Biology
  • Evolution, Molecular
  • Genome, Bacterial
  • Genomics
  • Multigene Family
  • Phylogeny
  • Reproducibility of Results
  • Software
Sprache
eng
Country
England
Paginierung
e5
PII
4564799
Datum der Veröffentlichung
2018
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2019
Titel
panX: pan-genome analysis and exploration.
Sub types
  • Journal Article
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
46

Datenquelle: PubMed

Beziehungen:
Eigentum von

Werkzeuge