The SILVA ribosomal RNA database
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany. The SILVA team is located in Bremen, Germany.
For any question please send a message to: contact (at) arb-silva.de
If you find SILVA a useful resource for your research or applications please cite:
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. Nucl. Acids Res. 42:D643-D648
Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, Ludwig W (2017) 25 years of serving the community with ribosomal RNA gene reference databases and tools. J. Biotechnol.
Candidate Taxonomic Units:
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology volume 12, pages 635–645
If you use the TreeViewer:
Beccati A, Gerken J, Quast C, Yilmaz P, Glöckner FO (2017) SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees. BMC Bioinformatics 18:43
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
If you use SINA please cite:
Pruesse, E, Peplies, J and Glöckner, FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics, 28, 1823-1829
For primer evaluation consider:
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl. Acids Res. 41:e1
If you use ARB:
Westram R, Bader K, Pruesse E, Kumar Y, Meier H, Glöckner FO, Ludwig W (2011) ARB: a software environment for sequence data. In: de Bruijn FJ (ed) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. John Wiley & Sons, Inc., pp 399-406
Add the SILVA barcode (coding for www.arb-silva.de) and update the readers of your posters and flyers with the latest information on the SILVA webpage using their mobile devices (click on the logo or barcode to enlarge).