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
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
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
Next-generation Sequencing03:00

Next-generation Sequencing

87.9K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.9K
Sequences01:29

Sequences

499
Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
499
Sanger Sequencing01:57

Sanger Sequencing

800.8K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
800.8K

You might also read

Related Articles

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

Sort by
Same author

DNAzyme based three-way junction assay for antibody-free detection of locus-specific N<sup>6</sup>-methyladenosine modifications.

Biosensors & bioelectronics·2021
Same author

Proximity ligation assay mediated rolling circle amplification strategy for in situ amplified imaging of glycosylated PD-L1.

Analytical and bioanalytical chemistry·2021
Same author

Dihydroartemisinin Induces O-GlcNAcylation and Improves Cognitive Function in a Mouse Model of Tauopathy.

Journal of Alzheimer's disease : JAD·2021
Same author

SnRK1 stimulates the histone H3K27me3 demethylase JMJ705 to regulate a transcriptional switch to control energy homeostasis.

The Plant cell·2021
Same author

Intratumoral injection of caerin 1.1 and 1.9 peptides increases the efficacy of vaccinated TC-1 tumor-bearing mice with PD-1 blockade by modulating macrophage heterogeneity and the activation of CD8<sup>+</sup> T cells in the tumor microenvironment.

Clinical & translational immunology·2021
Same author

Tilting Behavior of Lamellar Ice Tip during Unidirectional Freezing of Aqueous Solutions.

Langmuir : the ACS journal of surfaces and colloids·2021
Same journal

Haplotype-based Parallel PBWT for Biobank Scale Data.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2026
Same journal

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2016
Same journal

The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2015
Same journal

Localized Principal Component Analysis based Curve Evolution: A Divide and Conquer Approach.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2014
Same journal

Multicore and GPU Algorithms for Nussinov RNA Folding.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2014
Same journal

PMS6: A Fast Algorithm for Motif Discovery.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences·2013
See all related articles

Related Experiment Video

Updated: May 4, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

7.7K

Pairwise Sequence Alignment for Very Long Sequences on GPUs.

Junjie Li1, Sanjay Ranka, Sartaj Sahni

  • 1Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611.

IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [Proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences
|December 17, 2013
PubMed
Summary
This summary is machine-generated.

We created faster GPU algorithms for the Smith-Waterman algorithm, significantly speeding up pairwise sequence alignment for very long DNA or protein sequences.

Keywords:
CUDAGPULong sequence alignmentSmith-Waterman algorithmlocal alignment

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
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

3.1K

Related Experiment Videos

Last Updated: May 4, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

7.7K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K
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

3.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Pairwise sequence alignment is fundamental in bioinformatics for understanding biological sequences.
  • The Smith-Waterman algorithm is a standard dynamic programming method for local sequence alignment.
  • Existing GPU implementations face challenges with very long sequences or specific parallelization strategies.

Purpose of the Study:

  • To develop novel single-GPU parallelizations of the Smith-Waterman algorithm.
  • To enable efficient alignment of very long biological sequences.
  • To improve the computational performance of pairwise sequence alignment.

Main Methods:

  • Implementation of novel parallel algorithms on a single Graphics Processing Unit (GPU).
  • Adaptation of the Smith-Waterman algorithm for efficient parallel execution.
  • Benchmarking against existing GPU-based sequence alignment methods.

Main Results:

  • Achieved an order of magnitude reduction in runtime compared to competing GPU algorithms.
  • Demonstrated the effectiveness of the developed parallelization strategies for long sequences.
  • Successfully computed both alignment scores and actual alignments.

Conclusions:

  • The novel single-GPU parallelizations offer significant speedups for Smith-Waterman sequence alignment.
  • These algorithms are particularly advantageous for aligning very long biological sequences.
  • The developed methods represent a substantial advancement in computational bioinformatics tools.