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Bioinformatics. 2016 Mar 15;32(6):929-31. doi: 10.1093/bioinformatics/btv681. Epub 2015 Nov 16.

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

Author information

1
Ribocon GmbH, Fahrenheitstraße. 1, 28359 Bremen, Germany.
2
Marine Microbiology Group, Mediterranean Institute for Advanced Studies, C/ Miquel Marqués, 21, 07190, Esporles, Spain.
3
Max Planck Institute for Marine Microbiology, Microbial Genomics and Bioinformatics Research Group, Celsiusstraße 1, 28359 Bremen, Germany and Jacobs University gGmbH Bremen, Department of Life Sciences and Chemistry, Campus Ring 1, 28759 Bremen, Germany.

Abstract

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.

PMID:
26576653
PMCID:
PMC5939971
DOI:
10.1093/bioinformatics/btv681
[Indexed for MEDLINE]
Free PMC Article

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