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

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...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

You might also read

Related Articles

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

Sort by
Same author

A comprehensive performance analysis of sequence-based within-sample testing NIPT methods.

PloS one·2023
Same author

WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis.

Diagnostics (Basel, Switzerland)·2022
Same author

BioDynaMo: a modular platform for high-performance agent-based simulation.

Bioinformatics (Oxford, England)·2021
Same author

On the Performance of Video Resolution, Motion and Dynamism in Transmission Using Near-Capacity Transceiver for Wireless Communication.

Entropy (Basel, Switzerland)·2021
Same author

QuASeR: Quantum Accelerated de novo DNA sequence reconstruction.

PloS one·2021
Same author

WhiskEras: A New Algorithm for Accurate Whisker Tracking.

Frontiers in cellular neuroscience·2020
Same journal

Analysis of End-Tidal CO2 Variability During Plateau Waves Episodes: An Information Theoretic Approach<sup></sup>.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
Same journal

AI and Tomosynthesis for Breast Cancer Molecular Subtyping: A step toward precision medicine<sup></sup>.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
Same journal

Towards Sustainable Protein Recovery from Biological Waste: Assessing Polyethersulfone-based Microfiltration.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
Same journal

Analysis of the cardiovascular response to standardized polymicrobial peritonitis experimental model.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
Same journal

Automated Wrist Ultrasound Image Bone Enhancement and Segmentation Using Deep Learning.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
Same journal

A Deep Learning approach for Depressive Symptoms assessment in Parkinson's disease patients using facial videos.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2025
See all related articles

Related Experiment Video

Updated: May 25, 2026

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

GPU-accelerated protein sequence alignment.

Laiq Hasan1, Marijn Kentie, Zaid Al-Ars

  • 1Computer Engineering Lab, TU Delft, The Netherlands. L.HASAN@TUDELFT.NL

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
|January 19, 2012
PubMed
Summary
This summary is machine-generated.

This study accelerates the Smith-Waterman (S-W) algorithm for protein sequence alignment using Graphics Processing Units (GPUs). The optimized implementation significantly improves performance for genetic database searches.

More Related Videos

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

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

Related Experiment Videos

Last Updated: May 25, 2026

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

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • The Smith-Waterman (S-W) algorithm is a cornerstone for optimal local sequence alignment in bioinformatics.
  • Its application in large genetic and protein databases is computationally intensive.
  • Existing implementations face performance bottlenecks, limiting large-scale analyses.

Purpose of the Study:

  • To develop a Graphics Processing Units (GPUs) accelerated implementation of the Smith-Waterman algorithm.
  • To enhance the performance of protein sequence alignment for large biological databases.
  • To reduce memory access bottlenecks in sequence alignment computations.

Main Methods:

  • Implementation of the Smith-Waterman algorithm on Graphics Processing Units (GPUs).
  • Development of a novel sequence database organization strategy.
  • Application of memory access optimization techniques.

Main Results:

  • Achieved a performance of 21.4 Giga Cell Updates Per Second (GCUPS).
  • Demonstrated a 1.13x performance improvement over the state-of-the-art implementation.
  • Successfully reduced memory access overhead through optimized database organization.

Conclusions:

  • GPU acceleration offers a significant performance boost for the Smith-Waterman algorithm.
  • The proposed optimizations are effective in accelerating protein sequence alignment.
  • This enhanced implementation is suitable for large-scale genetic and protein database analysis.