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

The Nucleosome Core Particle02:10

The Nucleosome Core Particle

14.5K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
14.5K
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

2.4K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
2.4K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.8K
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...
4.8K
Global Climate Change01:50

Global Climate Change

28.9K
Throughout its ~4.5 billion year history, the Earth has experienced periods of warming and cooling. However, the current drastic increase in global temperatures is well outside of the Earth’s cyclic norms, and evidence for human-caused global climate change is compelling. Paleoclimatology, the study of ancient climate conditions, provides ample evidence for human-caused global climate change by comparing recent conditions with those in the past.
28.9K
Parallel Resonance01:23

Parallel Resonance

563
The parallel RLC circuit is an arrangement where the resistor (R), inductor (L), and capacitor (C) are all connected to the same nodes and, as a result, share the same voltage across them. The parallel RLC circuit is analyzed in terms of admittance (Y), which reflects the ease with which current can flow. The admittance is given by:
563
Parallel Processing01:20

Parallel Processing

724
The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
724

You might also read

Related Articles

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

Sort by
Same author

Accelign: a GPU-based library for accelerating pairwise sequence alignment.

BMC bioinformatics·2026
Same author

Post-Marketing Active Surveillance of Adverse Events Following Quadrivalent Subunit Influenza Vaccine in Healthy Participants Aged ≥ 3 Years in China.

Infectious diseases and therapy·2026
Same author

Deep learning automates Cobb angle measurement compared with multi-expert observers.

BJR artificial intelligence·2026
Same author

Evaluating Sociodemographic Biases in Artificial Intelligence-Based Glioblastoma Response Assessment Algorithms.

AJNR. American journal of neuroradiology·2026
Same author

Recyclable Thermoset Enabled by Copolymer of Elemental Sulfur and Acrylate With Controlled Disulfide Linkages.

Angewandte Chemie (International ed. in English)·2026
Same author

gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs.

IEEE transactions on computational biology and bioinformatics·2026
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Feb 2, 2026

Author Spotlight: Innovative Device Development for Advancing Dendroecology and Wood Anatomy Research
07:05

Author Spotlight: Innovative Device Development for Advancing Dendroecology and Wood Anatomy Research

Published on: September 27, 2024

3.0K

BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures.

Jikai Zhang1, Haidong Lan1, Yuandong Chan1

  • 1School of Software, Shandong University, Jinan, China.

Bioinformatics (Oxford, England)
|November 17, 2018
PubMed
Summary
This summary is machine-generated.

The BGSA toolkit offers optimized bit-parallel global pairwise alignment algorithms for faster analysis of large next-generation sequencing (NGS) datasets. This open-source toolkit significantly outperforms existing methods on various modern processors.

More Related Videos

Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis
06:56

Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis

Published on: September 22, 2023

1.7K
Evaluating the Function of the Foot Core System in the Elderly
08:25

Evaluating the Function of the Foot Core System in the Elderly

Published on: March 11, 2022

3.3K

Related Experiment Videos

Last Updated: Feb 2, 2026

Author Spotlight: Innovative Device Development for Advancing Dendroecology and Wood Anatomy Research
07:05

Author Spotlight: Innovative Device Development for Advancing Dendroecology and Wood Anatomy Research

Published on: September 27, 2024

3.0K
Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis
06:56

Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis

Published on: September 22, 2023

1.7K
Evaluating the Function of the Foot Core System in the Elderly
08:25

Evaluating the Function of the Foot Core System in the Elderly

Published on: March 11, 2022

3.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing large-scale next-generation sequencing (NGS) datasets requires efficient sequence alignment algorithms.
  • Existing tools often face performance bottlenecks with increasing data size.

Purpose of the Study:

  • To present the BGSA toolkit, featuring optimized implementations of bit-parallel global pairwise alignment algorithms.
  • To enhance the speed and efficiency of bioinformatics tools for NGS data analysis.

Main Methods:

  • Implementation of popular bit-parallel global pairwise alignment algorithms.
  • Optimization for modern multi-core CPUs and many-core CPUs (e.g., Xeon Phi).
  • Benchmarking against established tools like Edlib, SeqAn, BitPAl, and Parasail.

Main Results:

  • BGSA demonstrates superior performance in pairwise edit distance computations and general scoring schemes compared to Edlib, SeqAn, BitPAl, and Parasail.
  • On a Xeon Phi-7210, BGSA's banded edit distance performance is 4.4 times faster than NVBio on a Titan X GPU for read mapper seed verification.
  • Achieves significant speedups on both standard multi-core and Xeon Phi many-core processors.

Conclusions:

  • The BGSA toolkit provides a highly optimized solution for accelerating sequence alignment in bioinformatics.
  • BGSA offers substantial performance gains, particularly for large-scale NGS data analysis and read mapping applications.
  • The open-source availability facilitates adoption and further development in the research community.