JSpeciesWS is a ready-to-use web-based service to measure the probability if two or more prokaryotic genomes belong to the same species or not by pairwise comparison of their complete or draft nucleotide sequences.
In addition, a search function is provided which allows to rapidly compare selected genomes against a comprehensive reference database.

For analysis, you can upload your own genomes or select them from our integrated reference database GenomesDB which represents a comprehensive selection of publicly available genome sequences. Its original core is based on Ensembl Bacteria (v37) by EMBL-EBI. We constantly update this initial set of 44k genomes from 2017, mainly with new type strains, and we also curate the dataset with a focus on taxonomic assignment.

JSpeciesWS is intended to support the daily work of taxonomists and to pave the way for a genome-based identification of microbial cultures/isolates also in routine applications in the era of high-throughput sequencing.

Main Service Features

Exemplaric view into our GenomesDB (click to enlarge).

• Integrated database of more than 68k publicly available reference genomes.
• Upload of own genomes for analysis (complete or draft.)
• Three different methods for pairwise genome comparison.
• Search against our entire GenomesDB.
• Detailed documentation and peer reviewed.

Background and Scope

DNA-DNA-hybridization (DDH) measures the degree of genomic similarity between two pools of DNA molecules and for nearly five decades it has been considered as the gold standard for genetic species delineation. Now, in times of cost-efficient sequencing with scientists having easy access to thousands of publicly available genome sequences, the species delineation based on user-friendly computational pairwise genome comparisons to determine Overall Genome Relatedness Indices (OGRI) has emerged as a valuable alternative. This approach has already been widely accepted by the scientific community and specialized tools like the stand-alone software JSpecies ( Richter and Rosselló-Móra, 2009 ) have proven to provide valuable OGRI results.

JSpecies Web Server (JSpeciesWS) is a web-based implementation of the core features of the original JSpecies software for easy user-access and extended functionality. It represents the latest development of JSpecies in terms of usability, flexibility, and efficiency. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well as correlation indexes of tetra-nucleotide signatures (Tetra) of full or draft genomes. In addition, it provides a Tetra Correlation Search function (TCS), which allows to rapidly compare selected genomes against a continuously updated reference database.