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Database on the structure of small subunit ribosomal RNA
Y Van de Peer1, E Robbrecht, S de Hoog
1Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium.
Nucleic Acids Research
|December 10, 1998
Summary
The Antwerp database now offers over 11,500 small subunit ribosomal RNA sequences. These sequences are aligned using a validated secondary structure model, aiding molecular evolution studies.
Area of Science:
- Microbiology
- Bioinformatics
- Molecular Biology
Background:
- Small subunit ribosomal RNA (SSU rRNA) is crucial for phylogenetic analysis.
- Comprehensive sequence databases are essential for studying microbial diversity and evolution.
- Previous databases may lack the scale or alignment accuracy needed for robust analysis.
Purpose of the Study:
- To present an updated and expanded Antwerp database of SSU rRNA sequences.
- To provide a high-quality, aligned dataset for research in molecular evolution and taxonomy.
- To facilitate access to curated SSU rRNA sequence data via the World Wide Web.
Main Methods:
- Compilation of over 11,500 complete or nearly complete SSU rRNA sequences.
- Alignment of sequences based on an established secondary structure model.
- Incorporation of literature references, accession numbers, and taxonomic information.
Main Results:
- A substantial collection of SSU rRNA sequences is now available.
- Sequence alignment is supported by observed compensating substitutions, enhancing reliability.
- The database includes comprehensive metadata for each sequence.
Conclusions:
- The Antwerp database serves as a valuable resource for researchers in microbiology and evolutionary biology.
- The curated and aligned SSU rRNA data supports taxonomic and phylogenetic investigations.
- Web accessibility of the database promotes wider scientific use and data sharing.