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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

You might also read

Related Articles

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

Sort by
Same author

Considerations in reviewing network meta-analyses of heterogeneous clinical trial designs: a methodological review in Crohn's disease and ulcerative colitis.

Crohn's & colitis 360·2026
Same author

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.

bioRxiv : the preprint server for biology·2026
Same author

The impact of global recruitment and country income on placebo rates in inflammatory bowel disease clinical trials.

Journal of Crohn's & colitis·2026
Same author

Proactive Fecal Calprotectin Home Monitoring in Ulcerative Colitis: Results of a Prospective Randomized Control Trial.

Gastroenterology·2026
Same author

Safely targeting combination TNF and IL-23 using a gut-restricted and orally delivered therapeutic approach: proof-of-concept for the development of SOR102 in ulcerative colitis.

Translational gastroenterology and hepatology·2026
Same author

Efficacy of Upadacitinib Retreatment or Dose Escalation After Loss of Response in Ulcerative Colitis: Data From the Open-Label Extension of the U-ACTIVATE Study.

Gastro hep advances·2026
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

Related Experiment Video

Updated: May 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

An efficient alignment algorithm for searching simple pseudoknots over long genomic sequence.

Christopher Ma1, Thomas K F Wong, T W Lam

  • 1Department of Computer Science, The University of Hong Kong, Rm 301, Chow Yei Ching Building, Pokfulam Road, Hong Kong. cccma@cs.hku.hk

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 1, 2012
PubMed
Summary
This summary is machine-generated.

This study presents a faster computational method for identifying noncoding RNA (ncRNA) candidates with pseudoknots. The new algorithm significantly speeds up the search for ncRNA structures within long DNA sequences.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Related Experiment Videos

Last Updated: May 20, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Structural alignment is effective for identifying noncoding RNA (ncRNA) candidates due to conserved secondary structures.
  • Pseudoknots in ncRNA structures significantly increase the complexity of alignment algorithms, with the fastest for simple pseudoknots running in O(mn3) time.
  • Current methods require extensive computation when searching for ncRNA candidates within long DNA sequences.

Purpose of the Study:

  • To develop an efficient algorithm for structural alignment of ncRNA with simple pseudoknots.
  • To improve the speed of identifying ncRNA candidates in large DNA sequences.

Main Methods:

  • Developed a novel, efficient algorithm for structural alignment of ncRNA containing simple pseudoknots.
  • Implemented an effective pruning strategy based on calculating lower bound scores for optimal alignment.
  • Integrated an estimation of maximum achievable scores to determine candidate pruning.

Main Results:

  • The new algorithm achieves a 10-fold speedup compared to existing methods for simple pseudoknot detection.
  • The pruning strategy effectively reduces computational complexity without sacrificing accuracy.
  • Demonstrated significant efficiency gains in locating ncRNA candidates within long genomic sequences.

Conclusions:

  • The developed algorithm offers a substantial improvement in the speed and efficiency of ncRNA structural alignment.
  • This advancement facilitates more rapid and effective identification of ncRNA candidates, particularly those with pseudoknots.
  • The pruning strategy provides a robust approach for optimizing complex structural alignment tasks in bioinformatics.