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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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EDTA titrations are usually carried out in highly basic conditions, where the fully deprotonated form of EDTA, Y4−, actively complexes with the free metal ions in the solution. Several metal ions precipitate as hydrous oxide (hydroxides, oxides, or oxyhydroxides) under these conditions, lowering the concentration of free metal ions in the solution. For this reason, auxiliary complexing agents or ligands such as ammonia, tartrate, citrate, or triethanolamine are used in EDTA titrations to...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Published on: June 17, 2012

Chado controller: advanced annotation management with a community annotation system.

Valentin Guignon1, Gaëtan Droc, Michael Alaux

  • 1CIRAD, UMR AGAP, F-34398 Montpellier, France. valentin.guignon@cirad.fr

Bioinformatics (Oxford, England)
|January 31, 2012
PubMed
Summary
This summary is machine-generated.

A new Chado Controller manages genomic data, ensuring compliance with database schemas and annotation tools. This system enhances data management, annotation monitoring, and version control for biological databases.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Database Management

Background:

  • The Chado database schema is a standard for genomic data.
  • Genome annotation requires robust management and version control.
  • Existing tools for annotation management can be cumbersome.

Purpose of the Study:

  • To develop a controller for managing Chado database schemas.
  • To enhance compatibility with genome annotation tools.
  • To improve the management of public and private genomic data.

Main Methods:

  • Developed a controller compliant with the Chado database schema.
  • Integrated with genome browsers (GBrowse) and annotation editors (Artemis, Apollo).
  • Utilized PostgreSQL and Perl for system implementation.

Main Results:

  • The controller facilitates management of public and private data.
  • It enables monitoring of manual annotation with controlled vocabularies and structural/functional controls.
  • The system stores versioned annotations for all modified features.

Conclusions:

  • The Chado Controller offers a comprehensive solution for genomic data management.
  • It ensures compatibility with established bioinformatics tools and standards.
  • The controller improves data integrity and accessibility in genomic research.