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Updated: Jul 10, 2026
08:23
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
Published on: February 18, 2022
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with
Elmar Pruesse1, Christian Quast, Katrin Knittel
1Microbial Genomics Group, Max Planck Institute for Marine Microbiology.
Nucleic Acids Research
|October 20, 2007
Summary
A new SILVA database offers curated, aligned ribosomal RNA (rRNA) sequences for Bacteria, Archaea, and Eukarya. This resource aids microbial diversity studies and phylogenetic reconstruction with quality-controlled data.
Area of Science:
- Microbiology
- Bioinformatics
- Molecular Biology
Background:
- Ribosomal RNA (rRNA) gene sequencing is crucial for microbial phylogenetic reconstruction and diversity analysis.
- Existing tools like the ARB software suite face challenges in maintaining comprehensive rRNA databases due to data proliferation.
Purpose of the Study:
- To introduce SILVA, a new centralized web resource for up-to-date, quality-controlled, aligned rRNA sequence databases.
- To provide researchers with reliable rRNA data for Bacteria, Archaea, and Eukarya domains.
Main Methods:
- Implementation of the SILVA system for data management and quality control of rRNA sequences.
- Inclusion of rich contextual information, taxonomic classifications, and valid nomenclature for all sequences.
- Development of two ARB-compatible datasets: reference (Ref) for in-depth analysis and comprehensive (Parc) for biodiversity studies.
Main Results:
- The SILVA database provides quality-controlled, aligned rRNA sequences with associated metadata.
- Release 91 (August 2007) contains 547,521 sequences (461,823 small subunit, 85,689 large subunit).
- Downloadable datasets cater to specific research needs, from phylogenetic analysis to biodiversity assessments.
Conclusions:
- SILVA serves as a vital, comprehensive resource for microbial ecology and evolutionary studies.
- The system addresses the limitations of previous rRNA databases, ensuring data accuracy and accessibility.
- SILVA facilitates advanced research in microbial diversity and phylogenetic analysis.
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