The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Open accessAbstract
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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“16S rRNA gene sequencing data was analyzed using Silva 115 and 123 (Quast et al., 2013).”
From Mechanisms underlying microbial-mediated changes in social behavior in mouse models of autism spectrum disorder (2019) · cites this paper as Quast et al., 2013
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QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,714
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Lagesen, K., Hallin, P., Rødland, E., Stærfeldt, H., Rognes, T., & Ussery, D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm160 · Cited by 5,965
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Pruesse, E., Peplies, J., & Glöckner, F. (2012) · Bioinform. · doi:10.1093/bioinformatics/bts252 · Cited by 2,989
Self-citationThe New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
Adl, S., Simpson, A., Farmer, M. A., Andersen, R., Anderson, O., Barta, J. R., Bowser, S., Brugerolle, G., Fensome, R., Fredericq, S., et al. (2005) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2005.00053.x · Cited by 1,749
Research works printed but not linked: 2
- Schweer, 2011, Qualitätsmanagement ribosomaler RNA sequencen in der SILVA datenbank
- Garrity, 2002, Taxonomic Outline of the Prokaryotes
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The neuroactive potential of the human gut microbiota in quality of life and depression
Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0337-x · Cited by 1,963
Metadata
- Authors
- Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O.
- Affiliations
- Max Planck Institute for Marine Microbiology (DE)
- Constructor University (DE)
- Corresponding author
- Glöckner, Frank Oliver
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-27
- Volume
- 41
- Issue
- D1
- Pages
- D590-D596
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3531112
- OpenAlex
- W2034285706
- Cited by
- 33,055
- References
- 24
- Citations by year
- 2026: 3407 · 2025: 4378 · 2024: 4486 · 2023: 4028 · 2022: 4123 · 2021: 3786 · 2020: 2909 · 2019: 1893 · 2018: 1366 · 2017: 959 · 2016: 753 · 2015: 497 · 2014: 317 · 2013: 122 · 2012: 4
- FWCI
- 121.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (cc-by)
- Funders
- Deutsche Forschungsgemeinschaft
- Max-Planck-Gesellschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- SILVA database, ribosomal RNA gene sequences, small subunit rRNA, large subunit rRNA, sequencing quality control, bacterial classification, web-based tool
- MeSH terms
- Archaea, Bacteria, Software, Internet, Genes, rRNA, Databases, Nucleic Acid, Eukaryota, High-Throughput Nucleotide Sequencing
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