SILVA ribosomal RNA database
SILVA is a ribosomal RNA database established in collaboration between the Microbial Genomics Group at the Max Planck Institute for Marine Microbiology in Bremen, Germany, the Department of Microbiology at the Technical University Munich, and Ribocon.
Release 117 of the database (January 2014) held more than 4,000,000 small subunit (SSU - 16S/18S) and 400,000 large subunit (LSU - 23S/28S) sequences. Sequences are provided as files for the ARB software environment.
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596.
- Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Acids Res. 42:D643-D648
- The first SILVA paper: Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl. Acids Res. 35:7188-7196
- Chapter 6: An Introduction to RNA Databases by Marc P. Hoeppner, Lars E. Barquist, and Paul P. Gardner. "We present an introduction to RNA databases. The history and technology behind RNA databases is briefly discussed. We examine differing methods of data collection and curation, and discuss their impact on both the scope and accuracy of the resulting databases. Finally, we demonstrate these principals through detailed examination of four leading RNA databases: Noncode, miRBase, Rfam, and SILVA."
- Silva rRNA database project - A web based resource for ribosomal RNA sequence data
- Microbial Genomics Group website
- Chapter 6: An Introduction to RNA Databases by Marc P. Hoeppner, Lars E. Barquist, and Paul P. Gardner.
- The Silva ARB software and databases can be used by scientific community for free.
- Nucl. Acids Res. 41 (D1): D590-D596.
- Nucl. Acids Res. 42:D643-D648