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Related Concept Videos

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...
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-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jun 1, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Structator: fast index-based search for RNA sequence-structure patterns.

Fernando Meyer1, Stefan Kurtz, Rolf Backofen

  • 1Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

BMC Bioinformatics
|May 31, 2011
PubMed
Summary
This summary is machine-generated.

We developed a new RNA sequence-structure pattern matching method using affix arrays, achieving sublinear time complexity. This novel approach significantly accelerates searches in large RNA sequence databases, outperforming existing tools.

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Related Experiment Videos

Last Updated: Jun 1, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

AQRNA-seq for Quantifying Small RNAs
05:12

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
10:52

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • RNA secondary structure is crucial for function and often more conserved than sequence.
  • Efficiently searching RNA sequence-structure patterns in large databases is a significant challenge.
  • Current methods are limited by linear running times and cannot fully leverage RNA structural constraints.

Purpose of the Study:

  • To develop a novel, time-efficient method for matching RNA sequence-structure patterns in sequence databases.
  • To improve upon the limitations of existing RNA database search tools.

Main Methods:

  • Utilized affix arrays, a novel index data structure, for preprocessing sequence databases.
  • Implemented a bidirectional search strategy to handle RNA structural constraints effectively.
  • Introduced a chaining approach to manage complex secondary structures and filter spurious matches.

Main Results:

  • Achieved sublinear expected running time for RNA sequence-structure pattern matching.
  • Demonstrated significant speed improvements, up to two orders of magnitude faster than previous methods in benchmark experiments.
  • Successfully handled complex RNA secondary structures with multiple ordered patterns.

Conclusions:

  • The new method offers a well-suited solution for large-scale RNA sequence-structure pattern matching due to its sublinear time complexity.
  • The chaining method efficiently handles matches for RNA molecules with multiple substructures.
  • Released Structator, a robust open-source software for index-based RNA sequence-structure pattern searching.