WASPS: web-assisted symbolic plasmid synteny server

Abstract

Motivation: 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.

Results: 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.

Availability and implementation: 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 information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Synteny map of plasmid pTN2 from T. nautili. The first six tracks correspond to genes predicted in the Fasta query sequence in the six reading frames with corresponding E-values. The following tracks refer to plasmids from the WASPS database sharing synteny with the submitted sequence. Gene orthology is indicated by consistent graphic symbolism throughout the map. Genes in white color are singletons, devoid of ortholog in the database. As indicated, plasmids maps are accurately drawn to scale