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This article is part of the supplement: Third Annual MCBIOS Conference. Bioinformatics: A Calculated Discovery

Open Access Proceedings

RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers

Venkata Thodima, Mehdi Pirooznia and Youping Deng*

Author Affiliations

Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA

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BMC Bioinformatics 2006, 7(Suppl 2):S6  doi:10.1186/1471-2105-7-S2-S6

Published: 26 September 2006

Abstract

Background

Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology.

Results

The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search.

Conclusion

This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at http://mfgn.usm.edu/ebl/riboapt/ webcite.