Ribosomal Database Project (RDP)

Ribosomal Database Project (RDP) provides a curated database of aligned and annotated small subunit ribosomal RNA (rRNA) sequences and computational services for microbial taxonomy, phylogeny, and community profiling.

Key Features:

• Extensive Sequence Database: Release 8.1 contains over 16,277 prokaryotic, 5,201 eukaryotic, and 1,503 mitochondrial small subunit rRNA sequences in a curated, aligned, and annotated format, and public beta 9.0 expands the repository to more than 50,000 annotated bacterial sequences.
• Analysis Tools: Provides a Hierarchy Browser for sequence search and selection and a Phylip Interface for phylogenetic tree building and visualization.
• Sequence Analysis Services: Includes probe checking, phylogenetic placement of user sequences, screening for chimeric rRNA sequences, automated alignment, and generation of similarity matrices.
• Experimental Planning Tools: Offers resources for planning and analyzing terminal restriction fragment polymorphism (T-RFLP) experiments for microbial community profiling.

Scientific Applications:

• Microbial classification: Assignment and classification of prokaryotic, eukaryotic, and mitochondrial organisms based on small subunit rRNA sequences.
• Phylogenetic inference: Reconstruction and visualization of evolutionary relationships using aligned rRNA sequences and phylogenetic tree generation.
• Chimera screening and taxonomic accuracy: Detection of chimeric rRNA sequences to improve accuracy of taxonomic assignments and downstream analyses.
• Microbial ecology and metagenomics: Community profiling and support for T-RFLP-based analyses to study microbial diversity and composition.

Methodology:

Rigorous curation and annotation of rRNA sequences, regular database updates, and phylogenetic inference using algorithms that construct trees from aligned rRNA sequences.