JSpeciesWS Online Server for Genome-based Identification

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, based on the original JSpecies software (see Background below). In addition, a search function is provided which allows to rapidly compare selected genomes against a comprehensive reference database.

For analysis you can upload 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. That set of 44k genomes from 2017 we constantly augment with mainly new type strains and also curate 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-troughput sequencing.

If you have any questions or enquiries related to JSpeciesWS, please contact us at jspeciesws@ribocon.com.

  • integrated database of more than 50k publicly available reference genomes
  • further quality control and data integration on reference genomes
  • upload of own genome sequences for analysis (complete or draft)
  • three different analysis methods implemented for pairwise genome comparisons, plus search against entire reference database!
  • detailed documentation and full transparency; peer-reviewed
  • DNA-DNA-hybridization (DDH) measures the degree of genomic similarity between two pools of DNA molecules and since nearly 50 years it is considered as the gold standard for species delineation, despite the fact that distinct DDH determination methods frequently lead to different results (Rosselló-Móra and Amann, 2015). 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 (Chun and Rainey, 2014). 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.

    For data analysis, own genomes can be uploaded and/or references can be selected from the JSpeciesWS reference database. The service indicates whether two or more genomes share genomic identities above or below the species embracing thresholds, and serves as a fast way to allocate unknown genomes in the frame of the hitherto sequenced species. A single pairwise comparison is processed within few seconds and a matrix can be build for up to 15 genomes. Larger projects are afforded on request - contact us for a free personalized user account providing extended system access.

    Availability

    The service is freely available without registration
    (research use only):

    jspecies.ribohost.com/jspeciesws

    Uploaded genome sequences will only be analysed and not stored - data privacy is assured!

    Reference Database Status

    Our JSpeciesWS integrated reference database GenomesDB currently includes a total of

    50.854 genomes (January 2020)

    and is regularly updated by the latest type strains.

    Publication

    The tool has been published in 'Bioinformatics' in 2016 (open access) under the doi: 10.1093/bioinformatics/btv681

    JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.
    (Richter et al.)