Related Experiment Video
Updated: Jun 17, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
webMGR: an online tool for the multiple genome rearrangement problem
Chi Ho Lin1, Hao Zhao, Sean Harry Lowcay
1Genome Institute of Singapore, 60 Biopolis Street, #02-01, Genome, Singapore 138672.
Bioinformatics (Oxford, England)
|December 22, 2009
Summary
The MGR algorithm reconstructs genome evolution phylogenies. New heuristics significantly speed up this process, making evolutionary analysis more accessible, and a web server (webMGR) aids result navigation.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The MGR algorithm reconstructs phylogenetic trees based on gene or synteny block order across multiple genomes.
- Previous applications of MGR were limited by computationally intensive running times.
- A web server, webMGR, has been developed for accessing the MGR tool and its results.
Purpose of the Study:
- To improve the computational efficiency of the MGR algorithm.
- To enhance the usability of MGR for phylogenetic reconstruction.
- To provide a user-friendly web interface for analyzing genomic rearrangement data.
Main Methods:
- Development of novel heuristics to accelerate MGR's execution.
- Implementation of a web server (webMGR) for enhanced result visualization and navigation.
- Validation of improved algorithm accuracy alongside speed enhancements.
Main Results:
- Significant reduction in MGR's running time without sacrificing accuracy.
- Successful application of optimized MGR to diverse genomic datasets.
- Development of a comprehensive web interface for intuitive exploration of phylogenetic results.
Conclusions:
- The enhanced MGR algorithm offers a faster and more accurate method for reconstructing rearrangement phylogenies.
- webMGR provides an accessible platform for researchers to study genome evolution.
- The improved tool and web server facilitate broader application of phylogenetic analysis in genomics.
Related Concept Videos
02:53Conservative Site-specific Recombination and Phase Variation
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...
02:13Overview of Transposition and Recombination
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...
02:54Evolutionary Relationships through Genome Comparisons
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...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
02:37Gene Duplication and Divergence
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 characterized.
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 characterized.