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Related Concept Videos

RNA Structure01:23

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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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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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Efficient RNA structure comparison algorithms.

Abdullah N Arslan1, Jithendar Anandan1, Eric Fry1

  • 11 Department of Computer Science, Texas A&M University-Commerce, Commerce, TX 75428, USA.

Journal of Bioinformatics and Computational Biology
|November 9, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a fast algorithm for finding common RNA substructures using a novel representation and suffix array. The improved RNASSAC website now offers tools for RNA structure comparison and visualization.

Keywords:
RNA substructuremultiple RNA structure comparisonsuffix array algorithm

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • RNA secondary structure representation is crucial for database storage and substructure searching.
  • Existing methods for multiple RNA structure comparison are computationally intensive, often being NP-hard.

Purpose of the Study:

  • To develop a fast algorithm for identifying the largest common substructure among multiple RNA structures.
  • To introduce and efficiently solve a new, more strictly defined problem for comparing multiple RNA structures.
  • To enhance the RNASSAC website with improved tools for RNA structure analysis and visualization.

Main Methods:

  • Utilizing a relative addressing-based RNA secondary structure representation stored in a suffix array.
  • Implementing a fast substructure search algorithm based on binary search.
  • Developing iterative algorithms for finding large common and non-overlapping RNA substructures.

Main Results:

  • A novel, efficient algorithm for finding the largest common substructure in multiple RNA sequences.
  • Introduction of a new RNA structure comparison problem with a stricter similarity definition, efficiently solved.
  • Enhancement of the RNASSAC website with new search and drawing tools for RNA substructures and full structures.

Conclusions:

  • The proposed algorithms provide efficient solutions for multiple RNA structure comparison, addressing limitations of previous methods.
  • The enhanced RNASSAC website offers valuable new functionalities for researchers in RNA structure analysis.
  • This work facilitates faster and more comprehensive analysis of RNA structural similarities and differences.