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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.6K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.6K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.3K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.3K

You might also read

Related Articles

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

Sort by
Same author

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation.

Nucleic acids research·2026
Same author

Genomes from 117 vertebrate species reveal rapidly evolving segmental duplication landscapes.

bioRxiv : the preprint server for biology·2025
Same author

FGF12 Enhances Prostate Cancer Cell Survival via the YB1-lncRNA Axis.

Cells·2025
Same author

Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

Bioinformatics (Oxford, England)·2025
Same author

AI-driven 3D assessment for Peyronie's disease.

The journal of sexual medicine·2025
Same author

A comprehensive review and evaluation of species richness estimation.

Briefings in bioinformatics·2025

Related Experiment Video

Updated: Nov 19, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

410.5K

Detecting high-scoring local alignments in pangenome graphs.

Tizian Schulz1,2,3, Roland Wittler1,2, Sven Rahmann4

  • 1Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld 33615, Germany.

Bioinformatics (Oxford, England)
|February 3, 2021
PubMed
Summary

We developed a novel heuristic method for local DNA sequence alignment against pangenomes, enabling efficient, reference-free comparisons. This tool scales sublinearly with genome number, outperforming classical methods.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.5K

Related Experiment Videos

Last Updated: Nov 19, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

410.5K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.5K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pangenomic approaches are increasingly vital due to growing individual genome data.
  • Graphical representations like compacted colored de Bruijn graphs offer efficient pangenome storage and reference-free comparisons.
  • Existing tools lack local alignment search capabilities comparable to BLAST for graphical pangenomes.

Purpose of the Study:

  • To introduce a new heuristic method for finding maximum scoring local alignments of DNA sequences to graphical pangenomes.
  • To enable similarity comparisons between sequences within the pangenome.
  • To provide a scalable and efficient tool for pangenome analysis.

Main Methods:

  • A heuristic method for local alignment search against compacted colored de Bruijn graphs.
  • Statistical analysis to characterize local alignment scores and differentiate homology from spurious findings.
  • Implementation and performance evaluation of the proposed method.

Main Results:

  • The method successfully identifies maximum scoring local alignments in graphical pangenomes.
  • Local alignment scores exhibit an exponential-tail distribution, similar to BLAST.
  • The approach demonstrates sublinear scaling in time and memory usage with respect to the number of genomes.
  • The tool allows for intra-pangenome sequence similarity comparisons.

Conclusions:

  • The developed method provides a much-needed local alignment search tool for graphical pangenomes.
  • The heuristic approach is efficient and scalable, offering advantages over traditional methods.
  • The tool facilitates robust sequence similarity analysis within pangenomes, aiding genomic research.