The SILVA Ribosomal RNA Gene Database Project: Improved Data Processing and Web-based Tools

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 Nov 30

PMID 23193283

Citations 11422

Authors

Christian Quast

Elmar Pruesse

Pelin Yilmaz

Jan Gerken

Timmy Schweer

Pablo Yarza

Jorg Peplies

Frank Oliver Glockner

Affiliations

Soon will be listed here.

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.

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References

Munoz R, Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer K . Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol. 2011; 34(3):169-70. DOI: 10.1016/j.syapm.2011.03.001. View

Loy A, Maixner F, Wagner M, Horn M . probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res. 2006; 35(Database issue):D800-4. PMC: 1669758. DOI: 10.1093/nar/gkl856. View

Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K . The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. 2008; 31(4):241-50. DOI: 10.1016/j.syapm.2008.07.001. View

Meyer F, Paarmann D, DSouza M, Olson R, Glass E, Kubal M . The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9:386. PMC: 2563014. DOI: 10.1186/1471-2105-9-386. View

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

Pruesse E, Peplies J, Glockner F . SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012; 28(14):1823-9. PMC: 3389763. DOI: 10.1093/bioinformatics/bts252. View

Edgar R . Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26(19):2460-1. DOI: 10.1093/bioinformatics/btq461. View

Kottmann R, Kostadinov I, Duhaime M, Buttigieg P, Yilmaz P, Hankeln W . Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res. 2009; 38(Database issue):D391-5. PMC: 2808895. DOI: 10.1093/nar/gkp918. View

Euzeby J . List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol. 1997; 47(2):590-2. DOI: 10.1099/00207713-47-2-590. View

10.

Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R . The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2008; 37(Database issue):D141-5. PMC: 2686447. DOI: 10.1093/nar/gkn879. View

11.

Kohler T, Stingl U, Meuser K, Brune A . Novel lineages of Planctomycetes densely colonize the alkaline gut of soil-feeding termites (Cubitermes spp.). Environ Microbiol. 2008; 10(5):1260-70. DOI: 10.1111/j.1462-2920.2007.01540.x. View

12.

Takai K, Moser D, DeFlaun M, Onstott T, Fredrickson J . Archaeal diversity in waters from deep South African gold mines. Appl Environ Microbiol. 2001; 67(12):5750-60. PMC: 93369. DOI: 10.1128/AEM.67.21.5750-5760.2001. View

13.

Cochrane G, Karsch-Mizrachi I, Nakamura Y . The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2010; 39(Database issue):D15-8. PMC: 3013722. DOI: 10.1093/nar/gkq1150. View

14.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View

15.

Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar . ARB: a software environment for sequence data. Nucleic Acids Res. 2004; 32(4):1363-71. PMC: 390282. DOI: 10.1093/nar/gkh293. View

16.

Caporaso J, Kuczynski J, Stombaugh J, Bittinger K, Bushman F, Costello E . QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7(5):335-6. PMC: 3156573. DOI: 10.1038/nmeth.f.303. View

17.

Adl S, Simpson A, Farmer M, Andersen R, Anderson O, Barta J . The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005; 52(5):399-451. DOI: 10.1111/j.1550-7408.2005.00053.x. View

18.

Cole J, Chai B, Farris R, Wang Q, Kulam-Syed-Mohideen A, McGarrell D . The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 2006; 35(Database issue):D169-72. PMC: 1669760. DOI: 10.1093/nar/gkl889. View

19.

Lagesen K, Hallin P, Rodland E, Staerfeldt H, Rognes T, Ussery D . RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35(9):3100-8. PMC: 1888812. DOI: 10.1093/nar/gkm160. View