WASPS: web-assisted symbolic plasmid synteny server

Author:

Badel Catherine1,Da Cunha Violette1,Catchpole Ryan1,Forterre Patrick12,Oberto Jacques1

Affiliation:

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

2. Département de Microbiologie, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris 75015, France

Abstract

AbstractMotivationComparative 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.ResultsWe 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.Availability and implementationWASPS 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 informationSupplementary data are available at Bioinformatics online.

Funder

CNRS and the European Research Council under the

European Union's Seventh Framework Program

Project EVOMOBIL - ERC

Ecole Normale Supérieure de Lyon

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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