Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA Editing

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

RNA Stability

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 Stability

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 Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

<i>Special Issue:</i> 13th International Conference on Computational Advances in Bio and Medical Sciences.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same author

Fast Algorithms for Computing Jaro Similarity.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same author

Design, synthesis, characterization, pharmacological evaluation and in silico ADMET and molecular docking and dynamics simulations of a novel series of N-substituted pyrazole from chalcone derivatives.

Scientific reports·2026

Same author

<i>Special Section:</i> 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023).

Journal of computational biology : a journal of computational molecular cell biology·2025

Same author

A frameshift-generated cancer neoepitope that controls tumor burden in prophylaxis as well as therapy.

Journal of immunology (Baltimore, Md. : 1950)·2025

Same author

Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis.

Scientific reports·2024

Search research articles

Related Experiment Video

Updated: Jun 12, 2026

A Nonsequencing Approach for the Rapid Detection of RNA Editing

A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Improved algorithms for parsing ESLTAGs: a grammatical model suitable for RNA pseudoknots.

Sanguthevar Rajasekaran¹, Sahar Al Seesi, Reda A Ammar

¹Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Rd., Unit 2155, Storrs, CT 06269-2155, USA. rajasek@engr.uconn.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|May 26, 2010

Summary

Efficient parsing algorithms for Simple Linear Tree Adjoining Grammars (SLTAGs) and Extended SLTAGs (ESLTAGs) were developed. These new algorithms improve RNA structure prediction by offering better performance than existing methods.

More Related Videos

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

Related Experiment Videos

Last Updated: Jun 12, 2026

A Nonsequencing Approach for the Rapid Detection of RNA Editing

A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

Area of Science:

Computational Biology
Bioinformatics
Formal Language Theory

Background:

Formal grammars are crucial for modeling biological systems, particularly RNA structures.
Simple Linear Tree Adjoining Grammars (SLTAGs) and Extended SLTAGs (ESLTAGs) are key formalisms for RNA structure analysis.
The efficiency of parsing algorithms directly impacts the performance of grammar-based biological modeling techniques.

Purpose of the Study:

To develop and present efficient parsing algorithms for SLTAGs and ESLTAGs.
To improve the computational efficiency of RNA structure prediction using formal grammars.

Main Methods:

Developed novel parsing algorithms for SLTAGs and ESLTAGs.
Analyzed the time and space complexity of the proposed algorithms, achieving O(min{m,n⁴}).
Compared the practical performance of the new algorithms against existing methods, including those by Uemura et al.

Main Results:

The proposed algorithms for SLTAGs and ESLTAGs parsing demonstrate an efficient time and space complexity of O(min{m,n⁴}).
Empirical results indicate that the new algorithms outperform the algorithms developed by Uemura et al. in practice.
The developed algorithms provide a more efficient approach to parsing grammars used in RNA structure modeling.

Conclusions:

The presented efficient parsing algorithms for SLTAGs and ESLTAGs offer significant practical performance improvements.
These advancements contribute to more effective computational tools for RNA structure prediction and analysis.
The study highlights the importance of algorithmic efficiency in the application of formal grammars to biological problems.