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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data


NAR Molecular Biology Database Collection entry number 1183
Yilmaz, Pelin; Wegener Parfrey, Laura; Yarza, Pablo; Gerken, Jan; Prüsse, Elmar; Quast, Christian; Schweer, Timmy; Peplies, Jörg; Ludwig, Wolfgang; Glöckner, Frank Oliver
1Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
2University Bremen, Center for Computing Technologies, D-28359, Germany
3Jacobs University Bremen gGmbH, D-28759, Germany
4Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
5Department for Microbiology, Technical University Munich, D-85354 Freising, Germany
6Ribocon GmbH, D-28359 Bremen, Germany

Database Description

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. To cope with the deluge of data, the SILVA system (from Latin silva, forest) was implemented to provide a central, comprehensive web resource for up to date, quality controlled databases of aligned small- and large subunit rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies and carry a rich set of process information. An intuitive ranking system allows the user to get a rapid overview about the quality of the sequences. SILVA is designed as a central comprehensive resource by integrating multiple taxonomic classifications and the latest validly described nomenclature as well as additional information, such as if a sequence was derived from a cultivated organism, a type strain, or belongs to a genome project. All databases are fully compatible with the widely used ARB software package for phylogenetic inference and probe design.

Acknowledgements

We would like to thank Ralf Westram for expert assistance with the ARB software suite. We would also thank James Cole and the RDP II team for help with Pintail and fruitful discussions. We are grateful for funding from the Max Planck Society.

References

Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W.G., Peplies, J. and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res., 35, 7188-7196.


Go to the abstract in the NAR 2014 Database Issue.
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