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

5.7K
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...
5.7K
Combinatorial Gene Control02:33

Combinatorial Gene Control

8.3K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.3K
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
Synteny and Evolution02:31

Synteny and Evolution

3.3K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.3K
Phylogenetic Trees03:21

Phylogenetic Trees

45.3K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.3K
Phylogeny01:23

Phylogeny

44.1K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
44.1K

You might also read

Related Articles

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

Sort by
Same authorSame journal

Haplotype-aware long-read error correction.

Algorithms for molecular biology : AMB·2026
Same author

Cannabidiol in Digital Fatigue: Neuroadaptive Mechanisms and Therapeutic Perspectives on Chronic Screen Exposure.

CNS & neurological disorders drug targets·2026
Same author

Synergistic Interplay Between Probiotic-coated Nanoparticles and Antimicrobial Peptides in Food Biochemistry: Engineering Bioremediation Agents for Heavy Metal Detoxification.

Recent advances in food, nutrition & agriculture·2026
Same author

Immunomodulatory Nanocarriers in Multiple Sclerosis: Dual Targeting of Microglia and Mitochondria for Precision Neurotherapy.

Anti-inflammatory & anti-allergy agents in medicinal chemistry·2026
Same author

Polythiophene Nanocomposites as Smart and Sustainable Materials: Advancements in Energy, Environmental, and Biomedical Technologies.

Anti-inflammatory & anti-allergy agents in medicinal chemistry·2026
Same author

Emerging Frontiers in Prostate Cancer Diagnostics: Nanolaser-Guided Nanotechnology and Computational Biology for Biomarker Surveillance.

Anti-cancer agents in medicinal chemistry·2026
Same journal

Extension of partial atom-to-atom maps: uniqueness and algorithms.

Algorithms for molecular biology : AMB·2026
Same journal

Lossless pangenome indexing using tag arrays.

Algorithms for molecular biology : AMB·2026
Same journal

Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer.

Algorithms for molecular biology : AMB·2026
Same journal

Probing transcription factor subsets in gene regulatory networks.

Algorithms for molecular biology : AMB·2026
Same journal

Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features.

Algorithms for molecular biology : AMB·2026
See all related articles

Related Experiment Video

Updated: Jul 4, 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

409.0K

Co-linear chaining on pangenome graphs.

Jyotshna Rajput1, Ghanshyam Chandra1, Chirag Jain2

  • 1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, Karnataka, India.

Algorithms for Molecular Biology : AMB
|January 26, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces the first exact algorithm for co-linear chaining on cyclic pangenome graphs, improving sequence alignment accuracy for complex genomes. The new method enhances genomic diversity representation and analysis.

Keywords:
Genome sequencingPath coverSequence alignmentVariation graph

More Related Videos

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
Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

14.5K

Related Experiment Videos

Last Updated: Jul 4, 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

409.0K
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
Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

14.5K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Pangenome reference graphs offer compact representation of species genetic diversity, surpassing linear references.
  • Efficiently aligning sequences to complex, cyclic pangenome graphs remains a significant computational challenge.
  • Existing co-linear chaining algorithms are effective for acyclic graphs but struggle with cycles.

Purpose of the Study:

  • To develop the first practical formulation and exact algorithm for co-linear chaining on cyclic pangenome graphs.
  • To address the limitations of current alignment techniques in handling genomic cycles.
  • To improve the accuracy of sequence alignment in complex pangenome structures.

Main Methods:

  • Developed a novel exact algorithm for co-linear chaining specifically designed for cyclic pangenome graphs.
  • Provided rigorous proofs for the algorithm's correctness and computational complexity.
  • Evaluated performance by aligning simulated human long reads to a cyclic pangenome graph derived from 95 human assemblies.

Main Results:

  • The proposed algorithm offers an exact solution for co-linear chaining on cyclic pangenome graphs.
  • Demonstrated significant accuracy improvements in sequence alignment compared to existing heuristic methods.
  • Empirical evaluation confirmed the algorithm's effectiveness on a human pangenome graph.

Conclusions:

  • The new algorithm provides a foundational method for accurate sequence alignment in cyclic pangenome graphs.
  • This advancement enables more precise analysis of genetic diversity within species.
  • The implementation is publicly available for further research and application.