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RiboaptDB: a comprehensive database of ribozymes and aptamers
Venkata Thodima1, Mehdi Pirooznia, Youping Deng
1Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA. youping.deng@usm.edu
BMC Bioinformatics
|November 23, 2006
Summary
RiboaptDB is a new database for artificial ribozymes and aptamers, crucial for understanding functional nucleic acids. It offers valuable insights for medicine and computational biology, compiling data from in vitro selection experiments.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Ribozymes are catalytic RNA molecules.
- Aptamers are DNA or RNA molecules selected via SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to bind specific targets.
- Aptamers and ribozymes have potential applications in medicine and technology due to their binding capabilities.
Purpose of the Study:
- To create a comprehensive database (RiboaptDB) for sequences of artificial ribozymes and aptamers.
- To provide a centralized resource for data generated through in vitro selection methods.
- To facilitate research in functional nucleic acids and their applications.
Main Methods:
- Inclusion of sequences generated by in vitro selection methods.
- Data compilation from 423 citations.
- Development of search features including general, feature-wise, and BLAST searches.
- Implementation of a user submission form for new data.
Main Results:
- RiboaptDB contains 4212 sequences: 370 artificial ribozyme sequences and 3842 aptamer sequences.
- The database includes data not found in public 'natural' sequence databases like GenBank.
- Exponential accumulation of sequence data from in vitro selection experiments is highlighted.
Conclusions:
- RiboaptDB serves as a repository for potentially therapeutic or diagnostic nucleic acid sequences.
- The database aids computational and theoretical biologists in understanding in vitro selection and sequence space distribution.
- RiboaptDB is regularly updated and publicly accessible for research purposes.
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