SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Top Cited Papers
Open Access
- 18 October 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 35 (21), 7188-7196
- https://doi.org/10.1093/nar/gkm864
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.Keywords
This publication has 26 references indexed in Scilit:
- The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public dataNucleic Acids Research, 2006
- Comparative Sequence Analysis and Oligonucleotide Probe Design Based on 23S rRNA Genes of Alphaproteobacteria from North Sea BacterioplanktonSystematic and Applied Microbiology, 2004
- ARB: a software environment for sequence dataNucleic Acids Research, 2004
- The European ribosomal RNA databaseNucleic Acids Research, 2004
- UniProt: the Universal Protein knowledgebaseNucleic Acids Research, 2004
- Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNABioinformatics, 2003
- DNA points the way ahead in taxonomyNature, 2002
- The European Large Subunit Ribosomal RNA DatabaseNucleic Acids Research, 2001
- Microbial Ecology and Evolution: A Ribosomal RNA ApproachAnnual Review of Microbiology, 1986
- A general method applicable to the search for similarities in the amino acid sequence of two proteinsJournal of Molecular Biology, 1970