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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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Self-citationThe International Nucleotide Sequence Database Collaboration
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Flagged first, then by citations
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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Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684
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MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116
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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