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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.
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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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...
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Multiple sugar molecules that may or may...

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Gene Ontology annotation quality analysis in model eukaryotes.

Teresia J Buza1, Fiona M McCarthy, Nan Wang

  • 1Department of Basic Sciences, Mississippi State University, Mississippi 39762, USA.

Nucleic Acids Research
|January 12, 2008
PubMed
Summary

A new GO Annotation Quality (GAQ) score quantifies Gene Ontology (GO) annotation quality, including breadth, detail, and evidence type. This score helps researchers assess GO data for biological processes and experimental systems.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Functional analysis using Gene Ontology (GO) is vital for interpreting array data.
  • Assessing the quantity and quality of GO annotations is challenging for researchers.
  • Lack of transparency regarding GO annotation sources and update dates hinders quality assessment.

Purpose of the Study:

  • To introduce a quantitative measure, the GO Annotation Quality (GAQ) score, for assessing GO annotation quality.
  • To provide researchers with a tool to evaluate the reliability of GO data for their specific research needs.
  • To aid GO biocurators in maintaining and optimizing annotation quality for relevant research communities.

Main Methods:

  • Developed the GO Annotation Quality (GAQ) score, incorporating annotation breadth, detail, and evidence type.
  • Applied the GAQ scoring method to a diverse set of eukaryotic organisms as a case study.
  • Demonstrated the utility of the GAQ score for tracking temporal changes in GO annotations.

Main Results:

  • The GAQ score provides a quantitative assessment of GO annotation quality.
  • The GAQ score enables tracking of GO annotation changes over time.
  • The GAQ score facilitates the evaluation of GO annotation quality for specific biological processes and experimental systems.

Conclusions:

  • The GAQ score offers a robust method for evaluating the quality of Gene Ontology annotations.
  • Researchers can use the GAQ score to quantitatively assess functional data for their experimental systems.
  • The GAQ score supports improved data quality and usability in functional genomics research.