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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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 Structure01:19

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 Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

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Related Experiment Video

Updated: Jun 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Efficient alignment of RNAs with pseudoknots using sequence alignment constraints.

Byung-Jun Yoon1

  • 1Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, USA. bjyoon@ece.tamu.edu

EURASIP Journal on Bioinformatics & Systems Biology
|April 25, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for RNA structural alignment using profile-HMMs to identify reliable "seed" regions. This approach significantly accelerates RNA alignment speed by up to 11 times without compromising accuracy.

Related Experiment Videos

Last Updated: Jun 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Accurate RNA alignment requires considering both primary sequence and secondary structure.
  • Existing algorithms for RNA secondary structure alignment face high computational complexity.
  • Effective alignment constraints are needed to reduce computation without losing accuracy.

Purpose of the Study:

  • To develop a new method for fast and accurate structural alignment of RNAs, including pseudoknots.
  • To identify effective alignment constraints that improve computational efficiency.
  • To enhance existing RNA alignment algorithms with novel constraint strategies.

Main Methods:

  • Utilizing profile-Hidden Markov Models (profile-HMMs) to identify high-confidence "seed" regions for alignment.
  • Estimating the positional range of bases outside the identified seed regions.
  • Developing sequence alignment constraints based on seed region locations and estimated positional ranges.
  • Integrating these constraints into a profile context-sensitive HMM (profile-csHMM) based alignment algorithm.

Main Results:

  • The proposed method successfully identifies reliable "seed" regions for RNA alignment.
  • Constraints derived from seed regions and positional estimates effectively guide the alignment process.
  • Experimental results demonstrate a speed-up of up to 11 times in RNA alignment.
  • Alignment accuracy is maintained despite the significant increase in speed.

Conclusions:

  • The novel constraint method significantly improves the speed of RNA structural alignment.
  • This approach offers a computationally efficient solution for aligning RNAs with complex structures, including pseudoknots.
  • The method provides a practical advancement for large-scale RNA sequence and structure analysis.