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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Updated: Mar 21, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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RNA motif search with data-driven element ordering.

Ladislav Rampášek1,2,3, Randi M Jimenez2, Andrej Lupták4

  • 1Department of Computer Science, University of Toronto, Toronto, M5R 3G4, ON, Canada.

BMC Bioinformatics
|May 19, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces RNArobo, a new RNA motif search tool that significantly speeds up the identification of functional RNAs in genomic sequences. The enhanced algorithm achieves over 100-fold speedup for complex motifs, aiding RNA discovery.

Keywords:
EntropyPseudoknotRNA motif searchSearch order

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • RNA motif search in long genomic sequences is crucial for identifying functional RNAs.
  • Traditional methods using backtracking algorithms are computationally intensive and NP-hard.
  • Existing tools struggle with complex RNA motifs and insertions in helical structures.

Purpose of the Study:

  • To develop a novel algorithm and tool for efficient RNA motif searching.
  • To enhance RNA motif characterization by allowing insertions in helices.
  • To significantly accelerate the search for complex RNA motifs, including those with pseudoknots.

Main Methods:

  • Designed a new RNA motif search algorithm.
  • Implemented the RNArobo tool, extending the RNAbob descriptor language.
  • Developed a principled approach to element ordering for improved search efficiency.

Main Results:

  • RNArobo enables better characterization of ribozymes and aptamers by allowing helix insertions.
  • Achieved over 100-fold speedup for complex motif searches compared to previous tools.
  • Demonstrated significant performance improvements for RNA motif discovery.

Conclusions:

  • A new, faster method for RNA motif search has been developed.
  • RNArobo provides crucial speed improvements for identifying complex RNA motifs with pseudoknots.
  • The tool is available online to facilitate RNA research.