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'''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]].<ref>[http://www.arb-silva.de/ Silva rRNA database project - A web based resource for ribosomal RNA sequence data]</ref><ref>[http://www.mpi-bremen.de/en/Microbial_Genomics_Group.html Microbial Genomics Group website]</ref>
'''SILVA''' is a [[ribosomal RNA]] database{{r|nar|nar2|nar3}} 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]].{{r|self|mpi}}


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.<ref name=hoepp/> Sequences are provided as files for the ARB software environment.<ref>[http://www.arb-home.de/ The Silva ARB software and databases can be used by scientific community for free.]</ref>
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.{{r|hoepp}}{{failed verification}} Sequences are provided as files for the ARB software environment.{{r|self}}


==See also==
==See also==
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==References==
==References==
* 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.<ref>[http://nar.oxfordjournals.org/content/41/D1/D590 Nucl. Acids Res. 41 (D1): D590-D596.]</ref>
* Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and [['The All-Species Living Tree' Project|"All-species Living Tree Project (LTP)"]] taxonomic frameworks. Acids Res. 42:D643-D648<ref>[http://nar.oxfordjournals.org/content/42/D1/D643.full Nucl. Acids Res. 42:D643-D648]</ref>
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* 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."<ref name=hoepp>[http://arxiv.org/ftp/arxiv/papers/1206/1206.4084.pdf Chapter 6: An Introduction to RNA Databases by Marc P. Hoeppner, Lars E. Barquist, and Paul P. Gardner.]</ref>


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{{reflist|refs=
==Notes==

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{{reflist}}
<ref name=hoepp>Marc P. Hoeppner, Lars E. Barquist, Paul P. Gardner (2014). [http://link.springer.com/protocol/10.1007/978-1-62703-709-9_6 An Introduction to RNA Databases]. ''Methods in Molecular Biology'' '''1097''': 107–123. {{doi|10.1007/978-1-62703-709-9_6}}.</ref>

<ref name=mpi>[http://www.mpi-bremen.de/en/Microbial_Genomics_Group.html Environmental Bioinformatics]. Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology. Accessed November 2016.{{third-party inline}}</ref>

<ref name=nar>Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner (2013). [http://nar.oxfordjournals.org/content/41/D1/D590.full The SILVA ribosomal RNA gene database project: improved data processing and web-based tools]. ''Nucleic Acids Research'' '''41''' (D1): D590-D596. {{doi|10.1093/nar/gks1219}}{{third-party inline}}</ref>

<ref name=nar2>Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner (2014).[http://nar.oxfordjournals.org/content/42/D1/D643.full The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks]. ''Nucleic Acids Research'' '''42''' (D1): D643-D648. {{doi|10.1093/nar/gkt1209}}{{third-party inline}}</ref>

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<ref name=nar3>Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M. Fuchs, Wolfgang Ludwig, Jörg Peplies, Frank Oliver Glöckner (2007). [http://nar.oxfordjournals.org/content/35/21/7188.full SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB]. ''Nucleic Acids Research'' '''35''' (21): 7188-7196. {{doi|10.1093/nar/gkm864}}{{third-party inline}}</ref>

<ref name=self>[http://www.arb-home.de/ Silva]. Ribocon GmbH. Accessed November 2016.{{self-published inline}}</ref>

}}


[[Category:Biological databases]]
[[Category:Biological databases]]

Revision as of 13:33, 19 November 2016

SILVA is a ribosomal RNA database[1][2][3] 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.[4][5]

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.[6][failed verification] Sequences are provided as files for the ARB software environment.[4]

See also

References

  1. ^ Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41 (D1): D590-D596. doi:10.1093/nar/gks1219[third-party source needed]
  2. ^ Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza, Jan Gerken, Elmar Pruesse, Christian Quast, Timmy Schweer, Jörg Peplies, Wolfgang Ludwig, Frank Oliver Glöckner (2014).The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research 42 (D1): D643-D648. doi:10.1093/nar/gkt1209[third-party source needed]
  3. ^ Elmar Pruesse, Christian Quast, Katrin Knittel, Bernhard M. Fuchs, Wolfgang Ludwig, Jörg Peplies, Frank Oliver Glöckner (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 35 (21): 7188-7196. doi:10.1093/nar/gkm864[third-party source needed]
  4. ^ a b Silva. Ribocon GmbH. Accessed November 2016.[self-published source?]
  5. ^ Environmental Bioinformatics. Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology. Accessed November 2016.[third-party source needed]
  6. ^ Marc P. Hoeppner, Lars E. Barquist, Paul P. Gardner (2014). An Introduction to RNA Databases. Methods in Molecular Biology 1097: 107–123. doi:10.1007/978-1-62703-709-9_6.
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