WASPS: web-assisted symbolic plasmid synteny server.

Computers Internet Plasmids Software Synteny

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
01 03 2020
Historique:
received: 09 05 2019
revised: 22 07 2019
accepted: 30 09 2019
pubmed: 8 10 2019
medline: 18 9 2020
entrez: 8 10 2019
Statut: ppublish

Résumé

Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches. We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences. WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btz745 PMID: 31589313 PMC: PMC7703779
pubmed: 31589313
pii: 5582648
doi: 10.1093/bioinformatics/btz745
pmc: PMC7703779
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1629-1631

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press.

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Auteurs

Catherine Badel (C)

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.

Violette Da Cunha (V)

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.

Ryan Catchpole (R)

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.

Patrick Forterre (P)

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.
Département de Microbiologie, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris 75015, France.

Jacques Oberto (J)

Microbiology Department, CEA, CNRS, Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Ordinateurs › WASPS: web-assisted symbolic plasmid synteny server.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Réseaux de communication entre ordinateurs › Internet › WASPS: web-assisted symbolic plasmid synteny server.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Plasmides › WASPS: web-assisted symbolic plasmid synteny server.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › WASPS: web-assisted symbolic plasmid synteny server.
questionsmedicales.fr › Phénomènes génétiques › Similitude de séquences › Similitude de séquences d'acides nucléiques › Synténie › WASPS: web-assisted symbolic plasmid synteny server.