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

4.9K
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...
4.9K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

14.6K
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...
14.6K
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

2.5K
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.
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...
2.5K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.9K
Design Example: Alignment of a Road Line Using GIS01:17

Design Example: Alignment of a Road Line Using GIS

358
The alignment of a road line using Geographic Information Systems (GIS) is a critical process in civil engineering, combining advanced technology with practical decision-making. This methodology begins with the collection of geospatial data, including information on land cover, geomorphology, drainage patterns, slope, and contour details. Such data is typically acquired through satellite imagery and GIS tools, offering a comprehensive understanding of the terrain.Once the data is gathered, it...
358
Sequences01:29

Sequences

309
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...
309

You might also read

Related Articles

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

Sort by
Same author

An Anaerobic Trickle-Bed Reactor Filled with Siporax™ as a Novel Approach for Biomethanation of Hydrogen and Carbon Dioxide.

Bioengineering (Basel, Switzerland)·2026
Same author

Three Novel Genomes Broaden the Wild Side of the <i>Capsicum</i> Pangenome.

Plant direct·2025
Same author

Highly efficient transgene-free ErCas12a RNP-protoplast genome editing and single-cell regeneration in Nicotiana benthamiana for glyco-engineering.

Plant biotechnology journal·2025
Same author

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding.

G3 (Bethesda, Md.)·2023
Same author

Phylogenomic analysis provides insights into <i>MADS-box</i> and <i>TCP</i> gene diversification and floral development of the Asteraceae, supported by <i>de novo</i> genome and transcriptome sequences from dandelion (<i>Taraxacum officinale</i>).

Frontiers in plant science·2023
Same author

Signal-based optical map alignment.

PloS one·2021
Same journal

Invaders taking over-Mollusc faunal change in volcanic barrier lakes of the Albertine Rift biodiversity hotspot.

PloS one·2026
Same journal

AI-driven molecular diversification and ligand-based optimization of macitentan derivatives targeting VEGFR1 and endothelin signaling pathways.

PloS one·2026
Same journal

Performance patterns and records in the world aquatics masters championships: Where do the most frequently represented nations among the top-ten masters swimmers come from?

PloS one·2026
Same journal

Modeling diurnal Temperature-Rainfall relationships under multicollinearity using PLS-SEM: A case study of Ghana.

PloS one·2026
Same journal

Organizational culture, social capital, and emergency capacity in primary healthcare institutions: A cross-sectional structural equation modeling study comparing ordinary and older communities.

PloS one·2026
Same journal

Impact of kidney function on the metabolome in the general population.

PloS one·2026
See all related articles

Related Experiment Video

Updated: Feb 16, 2026

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

3.3K

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

Sven Warris1,2, N Roshan N Timal3, Marcel Kempenaar1

  • 1Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences Groningen, Groningen, the Netherlands.

Plos One
|January 3, 2018
PubMed
Summary
This summary is machine-generated.

The new pyPaSWAS tool offers accessible, parallel Smith-Waterman (SW) sequence alignment across multiple hardware platforms, including GPUs. This Python-based application simplifies bioinformatics by enabling accurate alignments and promoting wider adoption of parallel computing.

More Related Videos

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
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Related Experiment Videos

Last Updated: Feb 16, 2026

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

3.3K
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
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • High-Performance Computing

Background:

  • Previous Smith-Waterman (SW) sequence alignment tools like PaSWAS were limited to NVIDIA GPUs, hindering wider adoption.
  • OpenCL offers broader hardware compatibility, and Python integration can simplify parallel computing in bioinformatics.

Purpose of the Study:

  • To develop a versatile SW sequence alignment tool that overcomes platform limitations.
  • To enhance the usability and accessibility of parallel computing in bioinformatics through Python.

Main Methods:

  • Developed pyPaSWAS, a novel application implementing parallel SW sequence alignment entirely in Python.
  • Utilized Python libraries for system configuration, I/O, and logging.
  • Ensured compatibility with multi-core systems and GPUs.

Main Results:

  • pyPaSWAS provides accurate SW sequence alignments across diverse hardware platforms.
  • The application supports affine gap penalties and allows inspection of alignment details.
  • Python integration facilitates easier use and further development.

Conclusions:

  • pyPaSWAS offers a user-friendly, Python-based solution for parallel SW sequence alignments on GPUs and multi-core systems.
  • Integrating Python with high-performance parallel languages is a viable strategy for computationally intensive bioinformatics algorithms.
  • This approach can foster greater adoption and extension of parallel computing in the field.