Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Sep 6;7 Suppl 2(Suppl 2):S6.
doi: 10.1186/1471-2105-7-S2-S6.

RiboaptDB: a comprehensive database of ribozymes and aptamers

Venkata Thodima  1 , Mehdi Pirooznia, Youping Deng
Affiliations

RiboaptDB: a comprehensive database of ribozymes and aptamers

Venkata Thodima et al. BMC Bioinformatics. .

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 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/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Schematic illustration of three tier architecture of the RiboaptDB.
Figure 2
Figure 2
The schema and the dataflow of the RiboaptDB.
Figure 3
Figure 3
Screenshot of the homepage of the RiboaptDB, an user friendly interface for the database.
Figure 4
Figure 4
Screenshot of the local BLAST page with default options.
Figure 5
Figure 5
View of experiment details.
Figure 6
Figure 6
View of the data submission form by the user.
See this image and copyright information in PMC

References

    1. Jaeger L. The New World of ribozymes. Curr Opin Struct Biol. 1997;7:324–335. doi: 10.1016/S0959-440X(97)80047-4. - DOI - PubMed
    1. Kumar PK, Ellington AD. Artificial evolution and natural ribozymes. Faseb J. 1995;9:1183–1195. - PubMed
    1. Stull RA, Szoka FC., Jr Antigene, ribozyme and aptamer nucleic acid drugs: progress and prospects. Pharm Res. 1995;12:465–483. doi: 10.1023/A:1016281324761. - DOI - PubMed
    1. Tang J, Breaker RR. Rational design of allosteric ribozymes. Chem Biol. 1997;4:453–459. doi: 10.1016/S1074-5521(97)90197-6. - DOI - PubMed
    1. Murakami H, Suga H. [Artificial ribozymes: selection and application for nonnatural amino acid mutagenesis] Tanpakushitsu Kakusan Koso. 2003;48:1511–1518. - PubMed

Publication types