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

FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

20.8K
Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
20.8K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.2K
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...
11.2K
Genomics02:02

Genomics

36.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.4K
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

43.9K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
43.9K
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

6.1K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.1K
Multiple Bar Graph01:07

Multiple Bar Graph

5.2K
As the name suggests, a multiple bar graph is the same as a bar graph but has multiple bars to depict relationships between different data values. One can include as many parameters as possible. However, each parameter must have the same unit of measurement.
Each bar or column in the multiple bar graph represents a data value. These graphs are used primarily in interrelating two or more sets of data. The categories of different kinds of data are listed along the horizontal or x-axis, whereas...
5.2K

You might also read

Related Articles

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

Sort by
Same author

Comparing metabolic engineering scenarios using simulated design-build-test-learn-cycles.

Frontiers in bioengineering and biotechnology·2026
Same author

Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.

Frontiers in microbiology·2026
Same author

Response to 'On using clustering statistics for assessing plasmid binning tools accuracy'.

Briefings in bioinformatics·2026
Same author

A conserved bacterial signature characterizes plant microbiome responses to drought.

Frontiers in microbiology·2026
Same author

Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.

PloS one·2026
Same author

Phylogenetic analysis reveals diversity in glycan biosynthesis in "<i>Candidatus</i> Accumulibacter".

Biofilm·2026

Related Experiment Video

Updated: Jul 12, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K

Pan-genome de Bruijn graph using the bidirectional FM-index.

Lore Depuydt1, Luca Renders2, Thomas Abeel3,4

  • 1Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, 9052, Ghent, Belgium. Lore.Depuydt@UGent.be.

BMC Bioinformatics
|October 26, 2023
PubMed
Summary

We developed a new memory-efficient pan-genome graph data structure using a bidirectional FM-index. This structure enables efficient graph navigation, subgraph visualization, and approximate pattern matching for genomic data analysis.

Keywords:
Approximate pattern matchingLossless alignmentPan-genome visualizationSearch schemesSequence-to-graph alignment

More Related Videos

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
12:36

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Published on: May 9, 2011

10.3K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.3K

Related Experiment Videos

Last Updated: Jul 12, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.2K
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
12:36

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Published on: May 9, 2011

10.3K
Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pan-genome graphs are crucial for analyzing multiple genomes, representing similarities and differences.
  • Existing explicit graph representations can be memory-intensive.
  • Implicit graph representations using unidirectional FM-indexes offer memory efficiency but have functional limitations.

Purpose of the Study:

  • To address the shortcomings of existing implicit pan-genome graph representations.
  • To develop a memory-efficient data structure for pan-genome graphs.
  • To enhance functionality for graph navigation and pattern matching.

Main Methods:

  • Implemented a pan-genome graph data structure based on the bidirectional FM-index.
  • Enabled constant-time graph navigation in both forward and backward directions.
  • Developed subgraph visualization and lossless approximate pattern matching algorithms.

Main Results:

  • The bidirectional FM-index based structure overcomes limitations of unidirectional approaches.
  • Basic graph navigation steps are achieved in constant time.
  • Efficient retrieval of approximate read matches within a specified edit distance is demonstrated.
  • Case studies showcase the utility of topological information through visualization and alignment.

Conclusions:

  • A memory-efficient pan-genome graph representation is proposed.
  • The structure supports subgraph visualization and lossless approximate pattern matching.
  • The Nexus software implementing this approach is publicly available.