Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Nonsense-mediated mRNA Decay02:27

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,...

You might also read

Related Articles

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

Sort by
Same author

PhageMind: generalized strain-level phage host range prediction via meta-learning.

Bioinformatics (Oxford, England)·2026
Same author

Electrochemical in-biosensing computing.

National science review·2026
Same author

A bioinspired photoelectrochemical synapse for neurotransmitter-mediated in-sensor computing.

Biosensors & bioelectronics·2026
Same author

Mitophagy in cisplatin-induced kidney injury: regulatory mechanisms and therapeutic targets.

Annals of medicine·2026
Same author

Linkage-aware inference of fitness from short-read time-series genomic data.

Virus evolution·2026
Same author

Enhanced detection of bladder cancer using combined circulating tumor cells, urine-derived epithelial cells, and molecular biomarkers.

Journal of cancer research and clinical oncology·2026

Related Experiment Video

Updated: May 14, 2026

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

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

Published on: August 18, 2018

Efficient known ncRNA search including pseudoknots.

Cheng Yuan1, Yanni Sun

  • 1Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA. yannisun@msu.edu

BMC Bioinformatics
|February 2, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a novel tool for identifying non-coding RNA (ncRNA) with pseudoknots, overcoming limitations of current methods. The new approach effectively searches genomes for crucial ncRNA structures, improving annotation accuracy.

More Related Videos

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Dual CRISPR-Interference Strategy for Targeting Synthetic Lethal Interactions Between Non-Coding RNAs in Cancer Cells
07:23

Dual CRISPR-Interference Strategy for Targeting Synthetic Lethal Interactions Between Non-Coding RNAs in Cancer Cells

Published on: May 30, 2025

Related Experiment Videos

Last Updated: May 14, 2026

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

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

Published on: August 18, 2018

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Dual CRISPR-Interference Strategy for Targeting Synthetic Lethal Interactions Between Non-Coding RNAs in Cancer Cells
07:23

Dual CRISPR-Interference Strategy for Targeting Synthetic Lethal Interactions Between Non-Coding RNAs in Cancer Cells

Published on: May 30, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genome-scale annotation of non-coding RNAs (ncRNAs) is crucial.
  • Current methods based on context-free grammar (CFG) fail to model pseudoknots effectively.
  • Ignoring pseudoknots leads to inaccurate identification of functional ncRNAs.

Purpose of the Study:

  • To develop a pseudoknot search tool for accurate ncRNA identification.
  • To address the limitations of existing CFG-based methods in detecting pseudoknots.

Main Methods:

  • Designed a pseudoknot search tool utilizing multiple simple sub-structures.
  • Sub-structures derived from knot-free and bifurcation-free structural motifs.
  • Tested on a 22-Mb region of the Maize Genome.

Main Results:

  • The developed tool demonstrates competitive performance compared to other pseudoknot search methods.
  • Successfully identified pseudoknot-containing ncRNAs in the tested genomic region.

Conclusions:

  • The sub-structure based tool enables effective and efficient genome-scale pseudoknot search.
  • Provides a valuable complementary tool to existing methods like Infernal.
  • Source code is available for broader research application.