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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.
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Nucleic Acids and Nucleotides01:20

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Deoxyribonucleic Acid (DNA)
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 the organelles such as chloroplasts and mitochondria. In...
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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Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide

J Y Semegni1, M Wamalwa, R Gaujoux

  • 1Computational Biology Group, Department of Clinical Laboratory Sciences, IIDMM, University of Cape Town, Observatory, Cape Town, South Africa. yves@cbio.uct.ac.za

Bioinformatics (Oxford, England)
|July 16, 2011
PubMed
Summary
This summary is machine-generated.

NASP (Nucleic Acid Structure Predictor) identifies evolutionarily conserved nucleic acid secondary structures. This computational tool aids in understanding biological functions by accurately predicting base pairings.

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Last Updated: May 31, 2026

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Molecular biology

Background:

  • Natural nucleic acid sequences often possess conserved secondary structures critical for biological functions.
  • Identifying these structures computationally is essential for experimental validation.

Purpose of the Study:

  • To introduce NASP (Nucleic Acid Structure Predictor), a novel computational tool.
  • To identify evolutionarily conserved, biologically relevant secondary structures in nucleic acid sequences.

Main Methods:

  • NASP integrates thermodynamic stability, base pair probabilities, alignment uncertainty, covarying sites, and evolutionary conservation.
  • It employs a recursive permutation-based approach to prioritize conserved structures.

Main Results:

  • NASP selectively identifies evolutionarily conserved secondary structures.
  • The tool outperforms other methods in predicting actual base pairings within alignments.

Conclusions:

  • NASP is a valuable computational resource for researchers studying nucleic acid structure-function relationships.
  • By focusing on conserved elements, NASP enhances the reliability of secondary structure predictions for biological relevance.