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

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

You might also read

Related Articles

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

Sort by

Same author

Influence of Basalt Fibers on the Crack Resistance of Asphalt Mixtures and Mechanism Analysis.

Materials (Basel, Switzerland)·2022

Same author

Bioinspired Adaptive, Elastic, and Conductive Graphene Structured Thin-Films Achieving High-Efficiency Underwater Detection and Vibration Perception.

Nano-micro letters·2022

Same author

Artemisinin potentiates apoptosis and triggers cell cycle arrest to attenuate malignant growth of salivary gland tumor cells.

Acta biochimica Polonica·2022

Same author

Novel ensemble intelligence methodologies for rockburst assessment in complex and variable environments.

Scientific reports·2022

Same author

Case Report: Uniportal Video-Assisted Thoracoscopic Parenchymal Sparing Secondary Carinal Resection and Reconstruction for the Treatment of Tracheobronchial Mucoepidermoid Carcinoma.

Frontiers in surgery·2022

Same author

Effects of embryonic exposure to fluxapyroxad on zebrafish (Danio rerio) ocular development.

Pesticide biochemistry and physiology·2022

Same journal

Mild oxidative stress and dietary epigenetic modulators direct DNA methylation remodeling toward stress-resilience pathways.

BMC genomics·2026

Same journal

Integrative ATAC-Seq and RNA-Seq analysis identifies key genes for intramuscular fat content in Laiwu pigs.

BMC genomics·2026

Same journal

A comprehensive long RNA landscape of multi-regional porcine lung-derived small extracellular vesicles.

BMC genomics·2026

Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026

Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026

Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 15, 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

Efficient sequential and parallel algorithms for finding edit distance based motifs.

Soumitra Pal¹, Peng Xiao¹, Sanguthevar Rajasekaran²

¹Department of Computer Science and Engineering, University of Connecticut, 371 Fairfield Road,, Storrs, 06269, CT, USA.

|August 25, 2016

Summary

This summary is machine-generated.

Novel algorithms for the (l,d) Edit-distance-based Motif Search (EMS) problem significantly improve computational efficiency. These new sequential and parallel methods offer substantial speedups, advancing the state-of-the-art in biological pattern discovery.

Keywords:

Edit distance Motif Radix sort Trie

More Related Videos

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

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

Published on: July 14, 2015

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Related Experiment Videos

Last Updated: Mar 15, 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

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

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

Published on: July 14, 2015

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

Area of Science:

Bioinformatics
Computational Biology
Algorithm Design

Background:

Motif search is crucial for identifying patterns in biological data.
The general motif search problem is computationally challenging, requiring efficient algorithms.
The (l,d) Edit-distance-based Motif Search (EMS) problem seeks motifs with a specified length and error tolerance.

Purpose of the Study:

To develop novel, exact, sequential, and parallel algorithms for the (l,d) Edit-distance-based Motif Search (EMS) problem.
To improve the efficiency and speed of solving the EMS problem compared to existing methods.
To introduce new techniques for neighborhood exploration and motif representation.

Main Methods:

Developed a novel neighborhood exploration technique focusing on candidates at distance 'd'.
Utilized a trie-based data structure for efficient storage and sorting in the sequential algorithm.
Employed arrays and a modified radix-sort for efficient sorting in the parallel algorithm for shared memory systems.

Main Results:

Sequential algorithms demonstrated over 20x speedup on instance (16,3) compared to the previous best algorithm.
Achieved significant speedups on other challenging instances like (9,2), (11,3), and (13,4).
The parallel algorithm exhibited over 600% scaling performance with 16 threads.

Conclusions:

The developed algorithms represent a significant advancement in the state-of-the-art for EMS solvers.
The introduced techniques are potentially applicable to related motif search problems like Planted Motif Search (PMS) and Simple Motif Search (SMS).
These efficient algorithms facilitate more effective pattern discovery in large biological datasets.