JSpeciesWS (Ribocon GmbH)
JSpeciesWS is an easy-to-access, cloud-based bioinformatics service for calculating the extent of identity between microbial genomes on the total DNA level in the field of microbial systematics. For this, three common computational approaches for pairwise genome comparison are provided to the user. Such parameters are meanwhile broadly used in the process of microbial species circumscription and related taxonomic considerations. In fact, enabled by the era of high-throughput DNA sequencing, the service mimics in silico (much faster and more accurate) a laboratory-based method which has represented the gold-standard for microbial species delineation for nearly 50 years before.
For data analysis, own genomes can be uploaded by the user and/or public references can be selected from the internal reference database, providing more than 50k quality-controlled bacterial genomes. By default, matrices based on the pairwise comparison of up to 15 different organisms are supported – larger projects are possible on request. In addition, a function is offered which allows to search a selected genome against the entire reference set for a list of the most identical organisms, thereby serving as a fast way to allocate yet unidentified or taxonomically ambiguous genomes in the context of the hitherto genome-sequenced bacterial species.
A previous analysis can be re-accessed and even continued using an anonymous session code which is created and shared with the user when starting the workflow. The service can be accessed using the following link:
Keywords: bioinformatics, genome comparison, microbial systematics, high-throughput DNA sequencing, bacterial species delineation
This service is provided by the de.NBI Industrial Forum member Ribocon GmbH and is fully free for users from both academia and industry, without registration. Neither development nor maintenance is funded by de.NBI