The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison
Open accessAbstract
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
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
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TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
Meier-Kolthoff, J. P., & Göker, M. (2019) · Nature Communications · doi:10.1038/s41467-019-10210-3 · Cited by 3,276
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
Moraru, C., Varsani, A., & Kropinski, A. M. (2020) · Viruses · doi:10.3390/v12111268 · Cited by 872
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan
Sichert, A., Corzett, C. H., Schechter, M. S., Unfried, F., Markert, S., Becher, D., Fernandez-Guerra, A., Liebeke, M., Schweder, T., Polz, M. F., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0720-2 · Cited by 325
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents.
Meier, D. V., Pjevac, P., Bach, W., Hourdez, S., Girguis, P. R., Vidoudez, C., Amann, R., & Meyerdierks, A. (2017) · The ISME Journal · doi:10.1038/ismej.2017.37 · Cited by 177
Kandasamy, S., Yoo, J., Yun, J., Lee, K.-H., Kang, H.-B., Kim, J.-E., Oh, M.-H., & Ham, J.-S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232214494 · Cited by 51
Metadata
- Authors
- Richter, M., Rosselló-Móra, R., Oliver Glöckner, F., & Peplies, J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-11-16
- Volume
- 32
- Issue
- 6
- Pages
- 929-931
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2175094144
- Cited by
- 2,932
- References
- 3
- FWCI
- 32.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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