Related Experiment Video
Updated: Jul 18, 2026
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
EGenBio: a data management system for evolutionary genomics and biodiversity
Laila A Nahum1, Matthew T Reynolds, Zhengyuan O Wang
1Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.
BMC Bioinformatics
|November 23, 2006
Summary
Evolutionary Genomics and Biodiversity (EGenBio) is a new system for managing and filtering large genomic sequence datasets. It aids in evolutionary analysis and biodiversity research by integrating alignments, trees, and visualization tools.
Area of Science:
- Evolutionary biology
- Genomics
- Biodiversity research
Background:
- Accurate analysis of evolutionary processes requires efficient management of large, diverse genomic sequence data.
- Existing tools often lack integrated capabilities for handling evolutionary genomics and biodiversity data.
Purpose of the Study:
- To develop a comprehensive system, Evolutionary Genomics and Biodiversity (EGenBio), for managing and filtering large genomic sequence datasets.
- To facilitate accurate analysis and inference of evolutionary processes and genomic changes.
Main Methods:
- EGenBio integrates curated sequence alignments and phylogenetic trees.
- It offers tools for selecting, modifying, and filtering alignments within its Genomics division.
- The system includes tree-based navigation for species searches and tools for analyzing sequences and alignments in Biodiversity and Evolution divisions.
Main Results:
- EGenBio provides a structured platform with three divisions: Evolution, Genomics, and Biodiversity.
- It supports annotation of alignments with analytical results and modification history (PRAED format).
- The system is built on MySQL relational databases and dynamic page generation, utilizing custom programs.
Conclusions:
- EGenBio serves as a unified platform for tools and resources.
- It simplifies combined analyses in evolution, genomics, and biodiversity research.
Related Concept Videos
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...
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
02:02Genomics
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...
01:20Applications of Molecular Taxonomy
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.