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RNA Structure

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...

Types of RNA

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...

RNA Structure

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...

Types of RNA

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...

RNA Structure

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...

Types of RNA

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

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Pairwise RNA structure comparison with stochastic context-free grammars.

I Holmes, G M Rubin

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

|April 4, 2002

Summary

We developed faster algorithms for aligning RNA sequences to Pairwise Stochastic Context-Free Grammars (Pair SCFGs), making conserved RNA structure prediction more efficient. Our method significantly reduces computational cost by using precomputed structures.

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Area of Science:

Bioinformatics
Computational Biology
Structural Bioinformatics

Background:

Pairwise Stochastic Context-Free Grammars (Pair SCFGs) are effective for identifying conserved RNA structures.
Unconstrained alignment to Pair SCFGs presents significant computational challenges, limiting their practical application.

Purpose of the Study:

To develop efficient dynamic programming algorithms for RNA sequence alignment to Pair SCFGs.
To reduce the time complexity of alignment by conditioning on precomputed structures.

Main Methods:

Modified dynamic programming algorithms for Pair SCFGs.
Incorporation of precomputed structural information to guide the alignment process.
Implementation of the developed algorithms into freely available software.

Main Results:

Significant reduction in the time complexity of aligning RNA sequences to Pair SCFGs.
Development of practical and efficient computational tools for RNA structure analysis.
Successful implementation of generalized Pair SCFG alignment algorithms.

Conclusions:

The developed algorithms offer a computationally feasible approach for RNA structure conservation analysis using Pair SCFGs.
The software implementation facilitates broader use of these advanced alignment techniques in biological research.
Conditioning on precomputed structures is a key strategy for overcoming computational bottlenecks in Pair SCFG alignment.