Related Experiment Video
Updated: Nov 30, 2025
15:07
VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
27.1K
A Path-Deformation Framework for Determining Weighted Genome Rearrangement Distance.
Sangeeta Bhatia1, Attila Egri-Nagy1, Stuart Serdoz1
1Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.
Frontiers in Genetics
|November 16, 2020
Summary
This study introduces a new group theory method to calculate bacterial genome rearrangement distances, considering weighted inversions. It generalizes previous methods by using rewriting systems and the Knuth-Bendix algorithm for optimal distance calculation.
Area of Science:
- Computational Biology
- Genomics
- Bioinformatics
Background:
- Traditional genome distance calculations often assume equal inversion probabilities.
- Existing group theory approaches are limited to very short inversions.
Purpose of the Study:
- To generalize genome rearrangement distance calculations using group theory for any weighting on inversions.
- To introduce rewriting systems and the Knuth-Bendix algorithm to genome rearrangement problems.
Main Methods:
- Utilizing group theory and rewriting systems for group theory.
- Applying the Knuth-Bendix algorithm to generate a confluent system of rewriting rules.
- Deforming initial genome paths to optimality using the generated rules.
Main Results:
- Established a generalized framework for calculating weighted inversion distances between bacterial genomes.
- Successfully applied the Knuth-Bendix algorithm to genome rearrangement for the first time.
- Demonstrated a method to deform initial genome paths to find minimal distances.
Conclusions:
- The developed group-theoretic approach provides a more flexible and generalized method for measuring genome rearrangement distances.
- The integration of rewriting systems and the Knuth-Bendix algorithm offers a novel computational tool for comparative genomics.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.7K
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...
6.7K
02:13Overview of Transposition and Recombination
18.2K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
18.2K
01:09Mutation, Gene Flow, and Genetic Drift
61.1K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
61.1K
02:37Gene Duplication and Divergence
7.5K
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...
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...
7.5K
02:53Conservative Site-specific Recombination and Phase Variation
6.4K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
The recognition sites for Cre recombinase called LoxP...
6.4K
02:08Gene Conversion
10.3K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.3K