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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Sequence Networks of Rotating Machines01:24

Sequence Networks of Rotating Machines

A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Mesh Analysis01:20

Mesh Analysis

Mesh analysis is a valuable method for simplifying circuit analysis using mesh currents as key circuit variables. Unlike nodal analysis, which focuses on determining unknown voltages, mesh analysis applies Kirchhoff's voltage law (KVL) to find unknown currents within a circuit. This method is particularly convenient in reducing the number of simultaneous equations that need to be solved.
A fundamental concept in mesh analysis is the definition of meshes and mesh currents. A mesh is a closed...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

You might also read

Related Articles

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

Sort by
Same author

Ambient Oxygen Concentration Enrichment When Using a Face Mask Connected to the Breathing Circuit Versus a Venturi Device: A Simulation Study.

Cureus·2025
Same author

Subcellular distribution of RAD23B controls XPC degradation and DNA damage repair in response to chemotherapy drugs.

Cellular signalling·2017
Same author

Ni-Catalyzed Reductive Cross-Coupling of Amides with Aryl Iodide Electrophiles via C-N Bond Activation.

Organic letters·2017
Same author

Performance evaluation of the FDA-approved Determine™ HIV-1/2 Ag/Ab Combo assay using plasma and whole blood specimens.

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology·2017
Same author

A quantum-rovibrational-state-selected study of the reaction in the collision energy range of 0.05-10.00 eV: translational, rotational, and vibrational energy effects.

Physical chemistry chemical physics : PCCP·2017
Same author

Conventional MRI features for predicting the clinical outcome of patients with invasive placenta.

Diagnostic and interventional radiology (Ankara, Turkey)·2017
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
Same journal

Correction: TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: May 24, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Parallel progressive multiple sequence alignment on reconfigurable meshes.

Ken D Nguyen1, Yi Pan, Ge Nong

  • 1Department of Information Technology, Clayton State University, Morrow, GA 30260, USA.

BMC Genomics
|February 29, 2012
PubMed
Summary
This summary is machine-generated.

This study presents a novel parallel multiple sequence alignment algorithm, achieving O(m) run-time complexity. This breakthrough significantly accelerates the analysis of vast biological sequence data, overcoming limitations of traditional computing models.

More Related Videos

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

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: May 24, 2026

Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

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

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Algorithm Design

Background:

  • Multiple sequence alignment is crucial for identifying related biological sequences and their significance.
  • Traditional methods are computationally intensive, struggling with the increasing volume of sequencing data.
  • There is a critical need for efficient parallel algorithms to handle large-scale sequence analysis.

Purpose of the Study:

  • To develop a highly efficient parallel algorithm for multiple sequence alignment.
  • To reduce the computational complexity of existing multiple sequence alignment methods.
  • To address the challenges posed by the exponential growth of biological sequence data.

Main Methods:

  • Designed O(1) run-time solutions for dynamic programming pair-wise alignment on a reconfigurable mesh computing model.
  • Combined parallel pair-wise alignment with novel parallel components for progressive multiple sequence alignment.
  • Developed a general solution for multiple sequence alignment with O(m x n4) processing units and O(m) time.

Main Results:

  • Reduced progressive multiple sequence alignment run-time complexity from O(m x n4) to O(m) using O(m x n3) processing units.
  • Achieved O(m) run-time for progressive multiple sequence alignment, a first in complete parallelization.
  • Introduced a parallel Longest Common Subsequence (LCS) algorithm with O(1) run-time using O(n3) processing units.

Conclusions:

  • This work represents the first complete parallelization of the progressive multiple sequence alignment algorithm with O(m) run-time.
  • The new parallel LCS algorithm offers significant improvements over existing constant-time solutions.
  • The developed algorithms provide a powerful tool for accelerating biological sequence analysis and discovery.