JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

By Michael Richter, Ramon Rosselló-Mora, Frank Oliver Glöckner, Jörg Peplies. Bioinform., 2015

2,629 citations recorded by the source corpus.

Abstract Summary: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. 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). In addition, it provides a Tetra Correlation Search function, which allows to rapidly compare selected genomes against a continuously updated reference database with currently about 32 000 published whole and draft genome sequences. For comparison, own genomes can be uploaded and references can be selected from the JSpeciesWS reference database. The service indicates whether two 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. Availability and implementation: JSpeciesWS is available at http://jspecies.ribohost.com/jspeciesws. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mrichter@ribocon.com

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f6e1d998a6017045b05618ada6b154f8bb434e36

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Citations in the corpus

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses (2020, methodology): “…Yoon et al. 2017; Han et al. 2016), OrthoANI (Lee et al. 2016), EMBOSS Stretcher (Ceyssens et al. 2009), Gegenees (Agren et al. 2012), JSpeciesWS (Richter et al. 2016), KI-S tool (https://f1000research.com/posters/7-147), PAirwise Sequence Comparison (PASC; (Bao et al. 2012; Bao et al. 2014),…”
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. (2018, methodology): “Several software tools for calculating the original ANI and its improved versions were developed for taxonomic purposes [5, 8, 9, 30].”
Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies (2017, background): “The tetra-nucleotide composition of WGAs has been successfully applied to the rapid comparison between genomic and metagenomic assemblies [17, 19].”