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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

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.
DNA Structure
DNA has a double-helix structure. The...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. 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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

On the approximation of optimal structures for RNA-RNA interaction.

Saad Mneimneh1

  • 1Department of Computer Science, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA. saad@hunter.cuny.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 31, 2009
PubMed
Summary

Predicting RNA-RNA interaction structures is crucial. This study introduces approximation algorithms, achieving 1/2 and 2/3 factors, and defines an entangler to bound suboptimality in dynamic programming approaches.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA-RNA interactions are fundamental to numerous biological processes.
  • Predictive algorithms for RNA complex structures are of significant interest.
  • Existing algorithms often rely on dynamic programming but may not yield optimal structures due to the NP-complete nature of the problem.

Purpose of the Study:

  • To characterize the suboptimality of RNA-RNA interaction structure prediction algorithms.
  • To develop and analyze approximation algorithms for RNA-RNA interaction structure prediction.

Main Methods:

  • Demonstration of constant factor approximation algorithms based on dynamic programming.
  • Development of specific 1/2 and 2/3 factor approximation algorithms.
  • Definition of an 'entangler' to analyze algorithm performance.

Main Results:

  • Established the existence of constant factor approximation algorithms for RNA-RNA interaction structure prediction.
  • Presented 1/2 and 2/3 factor approximation algorithms.
  • Proved that 2/3 is a theoretical upper bound for approximation factor in entangler-free solutions.

Conclusions:

  • Dynamic programming algorithms for RNA-RNA interaction structure prediction are suboptimal.
  • Approximation algorithms offer a viable approach to address this suboptimality.
  • The concept of an entangler provides theoretical bounds for algorithm performance.