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Database on the structure of small ribosomal subunit RNA
Y Van de Peer1, S Nicolaï, P De Rijk
1Departement Biochemie, Universiteit Antwerpen (UIA), Belgium.
Nucleic Acids Research
|January 1, 1996
Summary
The Antwerp database provides over 4300 small ribosomal subunit RNA sequences, aligned by secondary structure. This resource aids researchers studying ribosomal RNA structure and evolution.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Small ribosomal subunit RNA (srRNA) is crucial for protein synthesis and phylogenetic analysis.
- Accurate sequence alignment and structural information are essential for understanding srRNA function and evolution.
- Existing databases may lack comprehensive structural data or accessibility.
Purpose of the Study:
- To present the Antwerp database, a curated collection of srRNA nucleotide sequences.
- To provide a structured alignment based on a validated secondary structure model.
- To make this valuable resource accessible to the scientific community.
Main Methods:
- Compilation of over 4300 srRNA nucleotide sequences.
- Alignment of sequences based on an established secondary structure model.
- Corroboration of the secondary structure model using compensating substitutions.
- Inclusion of literature references, accession numbers, and taxonomic data.
Main Results:
- A comprehensive database of 4300+ srRNA sequences is available.
- Sequences are aligned according to a robust secondary structure model.
- The database integrates primary and secondary structure data with taxonomic and literature information.
Conclusions:
- The Antwerp database serves as a valuable, accessible resource for srRNA research.
- The integrated data facilitates studies in molecular biology, evolution, and comparative genomics.
- Availability via anonymous ftp and WWW enhances scientific collaboration and data sharing.