IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.

Détails

Ressource 1Télécharger: Bertelli2017NAR_IslandViewer4.pdf (695.99 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_D8A6D1AB7FE1
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Synthèse (review): revue aussi complète que possible des connaissances sur un sujet, rédigée à partir de l'analyse exhaustive des travaux publiés.
Collection
Publications
Titre
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Périodique
Nucleic acids research
Auteur(s)
Bertelli C., Laird M.R., Williams K.P., Lau B.Y., Hoad G., Winsor G.L., Brinkman FSL
Collaborateur(s)
Simon Fraser University Research Computing Group
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Statut éditorial
Publié
Date de publication
03/07/2017
Peer-reviewed
Oui
Volume
45
Numéro
W1
Pages
W30-W35
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
Résumé
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

Pubmed
Web of science
Open Access
Oui
Création de la notice
12/01/2018 11:21
Dernière modification de la notice
20/08/2019 15:58
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