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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

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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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RNA Structure01:23

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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...
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RNA Structure01:19

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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.
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Nucleic acids02:43

Nucleic acids

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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.
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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,...
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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.
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Nucleic Acids and Nucleotides01:20

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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).
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Analyzing and Building Nucleic Acid Structures with 3DNA
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JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

Jieming Shi1, Xi Li1,2, Min Dong1,3

  • 1Department of Biology, Miami University, Oxford, Ohio, United States of America.

Plos One
|June 6, 2017
PubMed
Summary
This summary is machine-generated.

JNSViewer is a new JavaScript tool for visualizing RNA and DNA secondary structures. It integrates prediction tools and genome browsers for interactive analysis of plant genomic data.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Limited JavaScript tools exist for interactive RNA/DNA secondary structure visualization on web platforms.
  • Web-based computational biology requires integrated solutions for structure prediction and annotation.

Purpose of the Study:

  • To develop JNSViewer, a JavaScript-based interactive web service for DNA/RNA secondary structure visualization.
  • To integrate popular secondary structure prediction tools and genome browsers for enhanced analysis.
  • To facilitate the visualization of nucleotide correspondence, dot-bracket data, structure graphs, and genic annotations.

Main Methods:

  • Developed JNSViewer as a highly interactive web service using JavaScript.
  • Integrated multiple DNA/RNA secondary structure prediction tools.
  • Incorporated genome browsers (JBrowse, BrowserGenome) for chromosomal and genic annotation visualization.
  • Enabled customized GFF annotation import and sub-sequence structure extraction.

Main Results:

  • JNSViewer provides precise, interactive correspondence between nucleotides, dot-bracket data, and structure graphs.
  • Users can perform predictions, add custom annotations, and analyze specific genomic segments.
  • Integration with genome browsers allows for comprehensive visualization of genomic context and secondary structures.
  • Predicted RNA structures for Arabidopsis thaliana using StructureFold and high-throughput data are available.

Conclusions:

  • JNSViewer offers a powerful, integrated platform for RNA/DNA secondary structure analysis in a web environment.
  • The tool enhances visualization and analysis capabilities for plant genomics and RNA structure studies.
  • JNSViewer serves as a valuable resource for researchers in bioinformatics and molecular biology.