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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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...
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...
Organization of Genes02:07

Organization of Genes

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Mining Gene Ontology Data with AGENDA.

Guvanch Ovezmyradov1, Qianhao Lu, Martin C Göpfert

  • 1Department of Cellular Neurobiology, Georg-August-University of Göttingen, Schwann-Schleiden Research Centre for Molecular Cell Biology, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.

Bioinformatics and Biology Insights
|May 4, 2012
PubMed
Summary

AGENDA is a new web tool for accessing Gene Ontology (GO) data. It enables users to compare gene lists across species using GO terms, aiding genetic information analysis.

Keywords:
Gene Ontologycomplex querycontrolled vocabularydata mininggene annotation

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • The Gene Ontology (GO) provides a standardized framework for describing gene and protein functions.
  • Efficiently accessing and comparing GO annotations across species is crucial for understanding biological systems.
  • Existing tools may lack comprehensive features for comparative analysis of GO data.

Purpose of the Study:

  • To introduce AGENDA (Application for mining Gene Ontology Data), a novel web-based tool.
  • To provide a user-friendly platform for retrieving and comparing gene lists associated with GO terms.
  • To facilitate comparative genomics and functional analysis across diverse species.

Main Methods:

  • Development of a web-based application (AGENDA) for GO database access.
  • Implementation of batch query functionality for simultaneous retrieval of gene lists.
  • Integration of features for comparing gene annotations across different species.
  • Inclusion of options for bookmarking, visualizing, and downloading search results.

Main Results:

  • AGENDA enables simultaneous retrieval and comparison of gene lists linked to various GO terms.
  • The tool supports batch queries for efficient data mining across multiple species.
  • Users can bookmark, visualize, and download comparative genetic information.
  • AGENDA is an open-source application freely available for non-commercial use.

Conclusions:

  • AGENDA offers a powerful and accessible solution for comparative analysis of Gene Ontology data.
  • The tool streamlines the process of exploring functional genomics information across species.
  • AGENDA supports researchers in advancing genetic information annotation and discovery.