Database on the structure of small ribosomal subunit RNA

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Small ribosomal subunit RNA (SSU rRNA) is crucial for protein synthesis and widely used in phylogenetic studies.
• Maintaining an updated and accessible database of SSU rRNA sequences is essential for biological research.
• Previous databases may have lacked comprehensive structural information or easy accessibility.

Purpose of the Study:

• To present the updated Antwerp database of small ribosomal subunit RNA sequences.
• To provide a structured and accessible resource for researchers studying ribosomal RNA.
• To enhance the utility of the database through integrated structural and taxonomic information.

Main Methods:

• Compiling over 6000 nucleotide sequences for small ribosomal subunit RNA.
• Aligning sequences based on an established secondary structure model.
• Corroborating the secondary structure model using observed compensating substitutions.
• Integrating literature references, accession numbers, and taxonomic data.
• Making the database accessible via the World Wide Web.

Main Results:

• The Antwerp database now includes more than 6000 SSU rRNA nucleotide sequences.
• Sequences are stored in an alignment reflecting a validated secondary structure model.
• Compensating substitutions support the accuracy of the secondary structure model.
• Comprehensive data, including taxonomic information and literature references, is compiled.

Conclusions:

• The Antwerp database serves as a valuable, up-to-date resource for SSU rRNA data.
• The integrated structural and taxonomic information enhances its utility for research.
• Web accessibility facilitates widespread use by the scientific community.