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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...

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Related Experiment Video

Updated: Jun 17, 2026

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
08:06

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

Published on: January 19, 2017

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Sean D Hooper1, Daniel Dalevi, Amrita Pati

  • 1Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA. sean.d.hooper@genpat.uu.se

Bioinformatics (Oxford, England)
|December 17, 2009
PubMed
Summary

This study introduces a gamma distribution model to estimate unsequenced genomic diversity in metagenomics. The model helps determine the efficacy of additional sequencing for uncovering microbial community DNA fragments.

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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Related Experiment Videos

Last Updated: Jun 17, 2026

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
08:06

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

Published on: January 19, 2017

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • Shotgun sequencing produces short DNA reads for organismal or metagenomic analysis.
  • Read assembly into contigs depends on read count, length, and genome abundance.
  • Low coverage in metagenomes hinders estimation of uncaptured genomic diversity.

Purpose of the Study:

  • To develop a statistical model for estimating unsequenced genomic diversity in metagenomes.
  • To assess the potential yield of additional sequencing efforts.
  • To provide a method for quantifying microbial community DNA fragments.

Main Methods:

  • Modeling metagenomes as a population of DNA fragments (bins).
  • Employing a gamma distribution to represent the bin population.
  • Evaluating model performance with simulated and real metagenomic datasets.

Main Results:

  • The gamma distribution model effectively fits metagenomic data.
  • The model allows estimation of unsequenced bins.
  • Demonstrated applicability on three diverse metagenomic datasets.

Conclusions:

  • The gamma distribution provides a flexible approach to metagenomic analysis.
  • This method aids in optimizing sequencing strategies for microbial community studies.
  • Enables better characterization of genomic diversity in complex samples.