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Database Commons - SILVA

SILVA

Citations: 3927

z-index 82.11

Short name SILVA
Full name High quality ribosomal RNA databases
Description A comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria,Archaea and Eukaryota domains. SILVA are the official databases of the software package ARB.
URL http://www.arb-silva.de/
Year founded 2007
Last update & version 2016-04-04    v126
Availability Free to all users
University/Institution hosted Max Planck Institute for Marine Microbiology
Address D-28359 Bremen,Germany
City Bremen
Province/State
Country/Region Germany
Contact name Pelin Yilmaz
Contact email fog@mpi-bremen.de
Data type(s)
Major organism(s)
Keyword(s)
  • rRNA
Publication(s)
  • The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. [PMID: 24293649]

    Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner
    Nucleic acids research 2014:42(Database issue)
    57 Citations (Google Scholar as of 2016-01-29)

    Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive 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. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

  • The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. [PMID: 23193283]

    Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner
    Nucleic acids research 2013:41(Database issue)
    966 Citations (Google Scholar as of 2016-01-28)

    Abstract: 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.

  • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. [PMID: 17947321]

    Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M Fuchs, Wolfgang Ludwig, Jörg Peplies, Frank Oliver Glöckner
    Nucleic acids research 2007:35(21)
    2904 Citations (Google Scholar as of 2016-08-23)

    Abstract: Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.

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200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
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200 OK2016-01-04

Tags

RNA
Archaea Bacteria Eukaryota
rRNA

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2016-08-23]
    • Lin Xia [2016-03-28]
    • Zhang Zhang [2016-01-29]
    • Jian Sang [2015-07-01]
    • Lin Xia [2015-06-28]
Stats