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

5.8K
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...
5.8K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

437
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
437
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.3K
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...
3.3K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

830
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...
830
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

10.5K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
10.5K

You might also read

Related Articles

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

Sort by
Same author

Entropy-Regularized Attention for Explainable Histological Classification with Convolutional and Hybrid Models.

Entropy (Basel, Switzerland)·2025
Same author

Classification of Multiple H&E Images via an Ensemble Computational Scheme.

Entropy (Basel, Switzerland)·2024
Same author

Features based on the percolation theory for quantification of non-Hodgkin lymphomas.

Computers in biology and medicine·2017
Same author

TGF-beta receptor mediated telomerase inhibition, telomere shortening and breast cancer cell senescence.

Protein & cell·2016
Same author

NodePM: a remote monitoring alert system for energy consumption using probabilistic techniques.

Sensors (Basel, Switzerland)·2014
Same author

Estrogen deficiency reversibly induces telomere shortening in mouse granulosa cells and ovarian aging in vivo.

Protein & cell·2011
Same journal

Evaluating a Novel Cell-Free Preservation Solution for Human Cardiomyocyte Protection: A Proof-of-Concept Study.

BioMed research international·2026
Same journal

Clinical Efficacy of Chinese Medicine in Treating Adult Henoch-Schönlein Purpura: A Meta-Analysis.

BioMed research international·2026
Same journal

RETRACTION: Rehabilitation Training and Resveratrol Improve the Recovery of Neurological and Motor Function in Rats after Cerebral Ischemic Injury through the Sirt1 Signaling Pathway.

BioMed research international·2026
Same journal

The Oncogenic and Tumor-Suppressive Roles of SNHG18: A Double-Edged Long Noncoding RNA in Cancer.

BioMed research international·2026
Same journal

Evaluation of LncRNA NEAT1 and MEG3 Expression Levels in Hospitalized COVID-19 Patients.

BioMed research international·2026
Same journal

Perceived Self-Efficacy and Its Determinants for Noncommunicable Disease Prevention Among Adults in Southern Ethiopia: A Community-Based Cross-Sectional Study.

BioMed research international·2026
See all related articles

Related Experiment Video

Updated: Apr 25, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

6.8K

An efficient parallel algorithm for multiple sequence similarities calculation using a low complexity method.

Evandro A Marucci1, Geraldo F D Zafalon1, Julio C Momente1

  • 1Department of Computer Science and Statistics, Sao Paulo State University, Rua Cristóvão Colombo 2265, 15054-000 São José do Rio Preto, SP, Brazil.

Biomed Research International
|August 21, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces a parallel k-mers counting algorithm for faster multiple sequence similarity calculations in genomics. The developed algorithm shows excellent scalability and nearly linear speedup, enhancing bioinformatics applications.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

14.3K

Related Experiment Videos

Last Updated: Apr 25, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

6.8K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

14.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genomic research generates vast amounts of sequence data, necessitating efficient comparative methods.
  • Calculating sequence similarities is crucial for numerous bioinformatics applications.
  • Handling large datasets requires combining low-complexity methods with parallel computing.

Purpose of the Study:

  • To develop a parallel algorithm for calculating multiple sequence similarities using k-mers counting.
  • To address the computational challenges posed by the increasing volume of genomic data.

Main Methods:

  • Implementation of a parallel algorithm based on the k-mers counting method.
  • Utilizing parallel computing to enhance the efficiency of similarity calculations.
  • Testing the algorithm's performance and scalability.

Main Results:

  • The developed parallel algorithm demonstrates very good scalability.
  • A nearly linear speedup was achieved, with a 12x speedup observed for 14 nodes.
  • The k-mers counting method provides efficient and biologically relevant results.

Conclusions:

  • The proposed parallel algorithm offers a significant improvement for multiple sequence similarity calculations.
  • This approach can be integrated into parallel versions of popular multiple sequence alignment tools like MAFFT and MUSCLE.
  • Efficient handling of large genomic datasets is achievable through parallel computing and optimized algorithms.