RiboaptDB: A comprehensive database of ribozymes and aptamers

Venkata Thodima, Mehdi Pirooznia, Youping Deng

Research output: Contribution to journalArticle

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/.

Original languageEnglish (US)
Article numberS6
JournalBMC Bioinformatics
Volume7
Issue numberSUPPL.2
DOIs
StatePublished - Sep 26 2006
Externally publishedYes

Fingerprint

Catalytic RNA
Databases
Nucleotide Aptamers
Nucleic acids
Nucleic Acids
Medicine
Inorganic Chemicals
Inorganic chemicals
Organic Chemicals
Molecules
Chemical compounds
Nucleic Acid Databases
Bioelectric potentials
Organic chemicals
Nucleotides
RNA
DNA
Experiments
Ligands
Technology

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

RiboaptDB : A comprehensive database of ribozymes and aptamers. / Thodima, Venkata; Pirooznia, Mehdi; Deng, Youping.

In: BMC Bioinformatics, Vol. 7, No. SUPPL.2, S6, 26.09.2006.

Research output: Contribution to journalArticle

Thodima, Venkata ; Pirooznia, Mehdi ; Deng, Youping. / RiboaptDB : A comprehensive database of ribozymes and aptamers. In: BMC Bioinformatics. 2006 ; Vol. 7, No. SUPPL.2.
@article{438982274da44204801e044a1fc87283,
title = "RiboaptDB: A comprehensive database of ribozymes and aptamers",
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/.",
author = "Venkata Thodima and Mehdi Pirooznia and Youping Deng",
year = "2006",
month = "9",
day = "26",
doi = "10.1186/1471-2105-7-S2-S6",
language = "English (US)",
volume = "7",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
number = "SUPPL.2",

}

TY - JOUR

T1 - RiboaptDB

T2 - A comprehensive database of ribozymes and aptamers

AU - Thodima, Venkata

AU - Pirooznia, Mehdi

AU - Deng, Youping

PY - 2006/9/26

Y1 - 2006/9/26

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=33947314593&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33947314593&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-7-S2-S6

DO - 10.1186/1471-2105-7-S2-S6

M3 - Article

C2 - 17118149

AN - SCOPUS:33947314593

VL - 7

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - SUPPL.2

M1 - S6

ER -