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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.
Chromosome Structure02:40

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...
Chromosome Structure02:40

Chromosome Structure

A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
The centromere is a DNA sequence that links sister chromatids. This is also where kinetochores, protein complexes to which spindle microtubules attach, are constructed after the chromosome is replicated. The kinetochores allow the spindle microtubules to move the chromosomes within the cell during cell division.
Telomeres consist of non-coding repetitive nucleotide...
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...
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? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
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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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Using Chado to store genome annotation data.

Pinglei Zhou1, David Emmert, Peili Zhang

  • 1Harvard University, Cambridge, Massachusetts, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

This chapter details using XORT software to manage biological data in Chado databases. It covers importing genome annotation data and exporting it for analysis and reporting.

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Area of Science:

  • Bioinformatics
  • Database Management
  • Genomics

Background:

  • Chado is a flexible relational database schema for biological data management.
  • Ontologies and modular design enhance Chado's adaptability for diverse needs.
  • XORT is the primary tool for data manipulation within Chado.

Purpose of the Study:

  • To describe protocols for importing genome annotation data into Chado.
  • To outline methods for exporting Chado data into various formats.
  • To facilitate data reporting and mining using Chado databases.

Main Methods:

  • Utilizing the XORT software tool for data transfer.
  • Employing the XML-based ChadoXML format for import/export.
  • Implementing specific protocols for genome annotation data handling.

Main Results:

  • Successful import of genome annotation data into Chado.
  • Demonstrated export of Chado data into multiple file formats.
  • Established procedures for data retrieval for reporting and mining.

Conclusions:

  • XORT and Chado provide a robust system for biological data management.
  • The described protocols enable efficient data integration and analysis.
  • Chado's flexibility supports various bioinformatics data management requirements.