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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 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 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-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...
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...

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Mining frequent stem patterns from unaligned RNA sequences.

Michiaki Hamada1, Koji Tsuda, Taku Kudo

  • 1Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2-43 Aomi, Koto-ku, Tokyo, Japan. hamada-michiaki@aist.go.jp

Bioinformatics (Oxford, England)
|August 16, 2006
PubMed
Summary
This summary is machine-generated.

RNAmine identifies all possible RNA secondary structure motifs using graph mining, aiding biologists in thorough analysis. This method offers improved accuracy and efficiency for motif detection in non-coding RNAs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Identifying RNA secondary structure motifs is crucial for non-coding RNA detection.
  • Current algorithms often provide limited motif outputs, hindering comprehensive biological analysis.

Purpose of the Study:

  • To develop a method for exhaustive detection of all possible RNA secondary structure motifs.
  • To provide biologists with a tool for thorough inspection of RNA sequence motifs.

Main Methods:

  • RNAmine utilizes a graph theoretic representation of RNA sequences.
  • Employs a graph mining algorithm to detect motifs exhaustively.
  • The problem is framed as finding frequent patterns in directed, labeled graphs.

Main Results:

  • RNAmine successfully detects all possible motifs, unlike methods focusing on a few.
  • Demonstrated favorable accuracy and efficiency in secondary structure prediction.
  • Performed competitively with state-of-the-art methods like CMFinder in local motif detection.

Conclusions:

  • RNAmine provides a comprehensive approach to RNA motif detection.
  • The method enhances the ability of biologists to analyze RNA structures.
  • Software availability is provided upon request for further research.