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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary 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...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
Gene Duplication and Divergence02:37

Gene 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.
Genomics02:02

Genomics

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...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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

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Published on: December 22, 2017

A web-based software system for dynamic gene cluster comparison across multiple genomes.

Kashi Vishwanath Revanna1, Vivek Krishnakumar, Qunfeng Dong

  • 1Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.

Bioinformatics (Oxford, England)
|February 12, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel web-based system for comparative genomics, enabling dynamic gene cluster analysis without extensive pre-computation. The tool aids researchers in efficiently exploring gene conservation across multiple genomes.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Comparative genomics typically relies on computationally intensive, pre-computed genome-wide comparisons.
  • Existing methods for identifying homologous genes are often inaccurate and difficult to update.

Purpose of the Study:

  • To develop a user-friendly, web-based software system for dynamic analysis of gene cluster conservation.
  • To provide a flexible alternative to pre-computation-heavy comparative genomics tools.

Main Methods:

  • Developed a web-based system allowing users to upload gene lists for dynamic searching.
  • Implemented a novel multi-genome browser for interactive visualization of gene cluster conservation.
  • Designed the system for customization across various genome sequences.

Main Results:

  • The system successfully avoids expensive genome-wide pre-computation.
  • Users can dynamically adjust search criteria for specific genes of interest.
  • Demonstrated usability across both prokaryotic and eukaryotic genomes.

Conclusions:

  • The developed software offers an efficient and accurate approach for investigating gene cluster conservation.
  • This dynamic system caters to the specific needs of molecular biologists interested in smaller gene sets.
  • The tool is adaptable and applicable to a wide range of genomic research.