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

DNA-only Transposons02:57

DNA-only Transposons

14.6K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.6K
DNA Isolation01:24

DNA Isolation

39.6K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
39.6K

You might also read

Related Articles

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

Sort by
Same author

Supplementation with long-chain polyunsaturated fatty acids to extremely preterm infants associates with development of the intestinal microbiota.

Pediatric research·2026
Same author

Multiomics analyses in young grade C molar incisor pattern periodontitis.

Journal of dentistry·2026
Same author

Urea supplementation is associated with holistic changes in suprathreshold non-volatile flavour perception through oral microbiome carbon metabolism.

NPJ science of food·2026
Same author

Stromal and endothelial transcriptional changes during progression from MGUS to myeloma and after treatment response.

Nature communications·2026
Same author

Suprathreshold non-volatile flavour perception is associated with multiple species rather than any single species via bacterial metabolism.

Journal of oral microbiology·2026
Same author

Blood multiomics reveal a dysregulated lipid mediator-mitochondrial network associated with the outcome of advanced cirrhosis.

Nature communications·2026

Related Experiment Video

Updated: Aug 7, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

319

Palidis: fast discovery of novel insertion sequences.

Victoria R Carr1,2, Solon P Pissis3,4, Peter Mullany5

  • 1Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

Microbial Genomics
|March 10, 2023
PubMed
Summary

Microbial insertion sequences are vital for genome diversity but underrepresented in databases. A new bioinformatics tool, Palidis, rapidly identifies these sequences in metagenomic data, discovering many novel elements and horizontal gene transfer events.

Keywords:
antimicrobial resistancehorizontal gene transferinsertion sequencesmetagenomemobile genetic elementtransposon

More Related Videos

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri
11:36

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Published on: September 23, 2017

16.1K
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

17.7K

Related Experiment Videos

Last Updated: Aug 7, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

319
Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri
11:36

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Published on: September 23, 2017

16.1K
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

17.7K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Microbial insertion sequences are mobile genetic elements critical for microbial genome evolution and diversity.
  • Current databases underrepresent insertion sequences due to challenges in their identification within complex microbiome communities.

Purpose of the Study:

  • To develop and present a bioinformatics pipeline, Palidis, for rapid and accurate identification of insertion sequences in metagenomic data.
  • To enhance the representation of microbial insertion sequences in public databases and facilitate the study of their role in microbial evolution.

Main Methods:

  • Developed Palidis, a bioinformatics pipeline that identifies insertion sequences by detecting inverted terminal repeat regions.
  • Applied Palidis to analyze 264 human metagenome datasets.
  • Queried the identified insertion sequences against a comprehensive database of isolate genomes.

Main Results:

  • Palidis successfully identified 879 unique insertion sequences from 264 human metagenomes.
  • A significant portion, 519 of the identified sequences, were novel and previously uncharacterized.
  • Analysis revealed evidence of horizontal gene transfer events across diverse bacterial classes.

Conclusions:

  • Palidis is an effective tool for rapidly identifying microbial insertion sequences in metagenomic data.
  • The study significantly expands the catalogue of known insertion sequences, with many novel discoveries.
  • The findings provide insights into horizontal gene transfer mediated by insertion sequences across bacterial populations.