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

Retrieval01:12

Retrieval

450
Retrieval is the process of getting information out of memory storage and back into conscious awareness. This ability is essential for daily tasks like brushing hair and teeth, driving to work, and performing job duties. Retrieval occurs in three ways: recall, recognition, and relearning.
Recall involves accessing information without cues, such as during an essay test, where individuals must retrieve facts and concepts from memory unaided. Another example is remembering the name of a colleague...
450
ER Retrieval Pathway01:45

ER Retrieval Pathway

4.8K
In the secretory pathway, vesicles transport proteins from one cellular compartment to another in forward transport to deliver the protein to its correct location. Occasionally, misfolded proteins and incorrect proteins escape their original compartments, and a retrieval pathway is used to return the escaped proteins to their original compartment.
The ER uses many checkpoints to prevent the entry of incorrectly folded or a resident protein as cargo onto a transport vesicle. These mechanisms...
4.8K
Plasmids01:28

Plasmids

2.6K
Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
2.6K
Design Example: Alignment of a Road Line Using GIS01:17

Design Example: Alignment of a Road Line Using GIS

350
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...
350
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
Sequences01:29

Sequences

281
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...
281

You might also read

Related Articles

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

Sort by
Same author

Linkage-aware inference of fitness from short-read time-series genomic data.

Virus evolution·2026
Same author

PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.

Nucleic acids research·2026
Same author

A metatranscriptome based approach to predict multidrug resistance phenotypes in Klebsiella pneumoniae without culturing.

Journal of global antimicrobial resistance·2026
Same author

Fast and accurate identification of emerging viral reassortment from genome sequences.

Nucleic acids research·2026
Same author

PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes.

Interdisciplinary sciences, computational life sciences·2026
Same author

Unraveling the activity of phage-carrying antibiotic resistance genes in constructed wetlands.

Frontiers in cellular and infection microbiology·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
Same journal

Mapping the landscape of allele-specific expression in porcine genomes.

Genome biology·2026
Same journal

Genomic sequence evolution underlying human neocortical interareal diversification.

Genome biology·2026
Same journal

Regulatory mechanisms driven by functional 3'-UTR variants in alcohol use disorder and related traits.

Genome biology·2026
Same journal

A longitudinal single-nucleus transcriptomic atlas of bovine placentation reveals dynamic cellular hierarchies and regulatory programs.

Genome biology·2026
See all related articles

Related Experiment Video

Updated: Feb 9, 2026

Author Spotlight: Advanced Techniques for Characterizing Tissue Mineralization in Bone Regeneration Research
07:29

Author Spotlight: Advanced Techniques for Characterizing Tissue Mineralization in Bone Regeneration Research

Published on: September 27, 2024

1.3K

PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment.

Yongxin Ji1, Jiaojiao Guan1, Herui Liao2

  • 1Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR (HKG), China.

Genome Biology
|February 7, 2026
PubMed
Summary
This summary is machine-generated.

PlasRAG is a new tool for characterizing plasmids, which are crucial in the rise of drug-resistant bacteria. It efficiently retrieves plasmid DNA using text queries and analyzes their properties.

Keywords:
Biomedical language modelsMulti-modal contrastive learningRetrieval-augmented generation (RAG)Sequence-to-text plasmid characterizationText-to-sequence plasmid retrieval

More Related Videos

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
15:28

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

20.8K
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 9, 2026

Author Spotlight: Advanced Techniques for Characterizing Tissue Mineralization in Bone Regeneration Research
07:29

Author Spotlight: Advanced Techniques for Characterizing Tissue Mineralization in Bone Regeneration Research

Published on: September 27, 2024

1.3K
Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
15:28

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

20.8K
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:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • Plasmids are key drivers of multidrug resistance and bacterial pathogenicity, presenting major clinical issues.
  • A large number of plasmids remain unannotated, hindering comprehensive understanding and characterization.
  • Efficient tools are needed to analyze plasmid properties and facilitate DNA retrieval.

Purpose of the Study:

  • To introduce PlasRAG, a novel computational tool for plasmid characterization and DNA retrieval.
  • To develop a method for integrating multi-faceted property analysis of plasmids.
  • To enable plasmid DNA retrieval based on textual queries.

Main Methods:

  • PlasRAG utilizes a bidirectional multi-modal information retrieval model.
  • The model aligns DNA sequences with textual data for enhanced analysis.
  • The tool integrates comprehensive property characterization of query plasmids.

Main Results:

  • PlasRAG demonstrates robust performance in plasmid property characterization.
  • The tool provides enhanced analytical capabilities for plasmid DNA.
  • Experimental validation confirms the effectiveness of PlasRAG's architectural design.

Conclusions:

  • PlasRAG offers an effective solution for the comprehensive characterization of unannotated plasmids.
  • The tool advances plasmid analysis by integrating sequence and text data.
  • PlasRAG addresses the limitations of traditional methods in plasmid research.