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Database on the structure of small ribosomal subunit RNA
Y Van de Peer1, A Caers, P De Rijk
1Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium.
Nucleic Acids Research
|February 21, 1998
Summary
The Antwerp database now offers over 8600 small ribosomal subunit RNA sequences. These sequences are aligned using a validated secondary structure model, aiding taxonomic and evolutionary studies.
Area of Science:
- Molecular Biology
- Bioinformatics
- Evolutionary Biology
Background:
- Small ribosomal subunit RNA (SSU rRNA) is crucial for phylogenetic analysis.
- Comprehensive sequence databases are essential for studying microbial diversity and evolution.
- Previous databases may have lacked sufficient sequence numbers or alignment accuracy.
Purpose of the Study:
- To present an updated and expanded database of small ribosomal subunit RNA sequences.
- To provide a reliable, aligned dataset for comparative analysis.
- To facilitate research in microbial taxonomy and molecular evolution.
Main Methods:
- Compilation of approximately 8600 complete or nearly complete SSU rRNA sequences.
- Alignment of sequences based on an established secondary structure model.
- Integration of literature references, accession numbers, and taxonomic data.
Main Results:
- A substantial collection of SSU rRNA sequences is now accessible.
- Sequence alignment is supported by compensating substitution evidence.
- The database includes comprehensive metadata for each sequence.
Conclusions:
- The Antwerp database provides a valuable resource for molecular biology research.
- The validated alignment enhances the reliability of phylogenetic inferences.
- The database is publicly accessible via the World Wide Web for global scientific use.