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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-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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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...
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...

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Use of Alu Element Containing Minigenes to Analyze Circular RNAs
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Murlet: a practical multiple alignment tool for structural RNA sequences.

Hisanori Kiryu1, Yasuo Tabei, Taishin Kin

  • 1Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. kiryu-h@aist.go.jp

Bioinformatics (Oxford, England)
|April 27, 2007
PubMed
Summary
This summary is machine-generated.

We developed an efficient algorithm for multiple RNA sequence alignment, improving upon the Sankoff algorithm. This method enhances alignment quality and consensus secondary structure prediction for structural RNA genes.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Structural RNA genes require accurate multiple alignments that account for conserved secondary structures.
  • The Sankoff algorithm considers base-pair covariation but is computationally expensive for most RNA sequences.

Purpose of the Study:

  • To develop an efficient algorithm for multiple alignment of structural RNA sequences.
  • To overcome the computational limitations of existing Sankoff-based algorithms.

Main Methods:

  • A variant of the Sankoff algorithm was developed using an efficient scoring system.
  • The algorithm computes match and base pairing probability matrices for scoring alignments.
  • External programs are used for consensus secondary structure prediction.

Main Results:

  • The proposed algorithm significantly reduces time and space requirements without compromising alignment quality.
  • It achieves superior alignment quality and consensus secondary structure prediction accuracy compared to other methods.
  • The algorithm successfully aligns longer RNA sequences, such as eukaryotic-type signal recognition particle RNA (approx. 300 nt).

Conclusions:

  • The developed algorithm, implemented as 'Murlet' software, provides an efficient and accurate solution for multiple structural RNA sequence alignment.
  • This advancement enables the analysis of previously intractable long RNA sequences.