SILVA rRNA database

SILVA rRNA database provides quality-controlled, aligned small subunit (SSU; 16S/18S) and large subunit (LSU; 23S/28S) ribosomal RNA gene sequence databases for phylogenetic inference and taxonomic classification across Bacteria, Archaea, and Eukaryota.

Key Features:

• Comprehensive aligned datasets: Aligned SSU (16S/18S) and LSU (23S/28S) rRNA sequence datasets covering Bacteria, Archaea, and Eukaryota with regular updates (releases at least annually).
• Quality control and manual taxonomy curation: Quality-control procedures and manually curated taxonomy based on representative phylogenetic trees for rRNA genes to support reliable classification in next-generation sequencing studies.
• SILVA Incremental Aligner (SINA): Multiple sequence alignment via SINA using k-mer searching and partial order alignment (POA), optimized for large volumes of rRNA sequences and reported to achieve higher alignment accuracy compared with PyNAST and mothur.
• Consistent nomenclature for environmental clades: Standardized naming conventions for clades of uncultivated environmental sequences to improve coverage and classification consistency across domains of life.

Scientific Applications:

• Phylogenetic inference: Reference alignments and curated taxonomies for reconstructing phylogenies using SSU and LSU rRNA genes.
• Taxonomic classification of sequencing data: Reference database for taxonomic assignment of rRNA sequences from next-generation sequencing and high-throughput studies.
• Biodiversity and microbial ecology: Baseline datasets for biodiversity analyses and microbial community profiling across environments.
• Medical and industrial applications: Support for applications in medical diagnostics, biotechnology, and quality control through curated rRNA sequence references.

Methodology:

Multiple sequence alignments computed with SINA using k-mer searching and partial order alignment (POA); manual taxonomy curation based on representative phylogenetic trees; implementation of quality-control procedures for rRNA sequences.