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Related Concept Videos

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 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...
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

ncRNA consensus secondary structure derivation using grammar strings.

Rujira Achawanantakun1, Yanni Sun, Seyedeh Shohreh Takyar

  • 1Computer Science and Engineering Department, Michigan State University, East Lansing, Michigan 48824, USA.

Journal of Bioinformatics and Computational Biology
|April 28, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces grammar strings, a new method for deriving noncoding RNA (ncRNA) secondary structures. This approach improves accuracy and efficiency in RNA structure modeling and alignment, outperforming existing tools.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Noncoding RNAs (ncRNAs) rely on both sequence and secondary structure for function.
  • Accurate secondary structure derivation is crucial for understanding ncRNA roles.
  • Existing comparative analysis tools for ncRNA structure annotation have limitations in efficiency and accuracy.

Purpose of the Study:

  • To develop a novel and efficient method for noncoding RNA (ncRNA) secondary structure modeling and alignment.
  • To introduce a new representation for ncRNA secondary structures called grammar strings.
  • To improve the accuracy of consensus secondary structure derivation for ncRNA families.

Main Methods:

  • Developed a novel ncRNA secondary structure representation: grammar strings.
  • Grammar strings encode ncRNA sequence and structure within a context-free grammar (CFG) parameter space.
  • Converted ncRNA alignment into sequence alignment using grammar strings for consensus structure derivation.

Main Results:

  • Derived consensus secondary structures for hundreds of ncRNA families from BraliBase 2.1.
  • Successfully analyzed 25 ncRNA families containing pseudoknots using grammar string alignment.
  • Grammar string-based structure derivation demonstrated competitive performance in consensus structure quality compared to Murlet and RNASampler.

Conclusions:

  • Grammar strings offer an efficient and accurate approach for noncoding RNA (ncRNA) secondary structure modeling and alignment.
  • The method effectively derives consensus secondary structures, including those with pseudoknots.
  • This novel representation advances the field of ncRNA research and computational structural biology.