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DNA Microarrays

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 28, 2026

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

Published on: April 25, 2014

In silico microarray probe design for diagnosis of multiple pathogens.

Ravi Vijaya Satya¹, Nela Zavaljevski, Kamal Kumar

¹Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. rvijaya@bioanalysis.org

|October 23, 2008

Summary

A new bioinformatics pipeline efficiently designs microarray probes for multiple pathogen genomes, speeding up the identification of common and unique genetic fingerprints. This method enhances pathogen detection and characterization for public health applications.

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Last Updated: Jun 28, 2026

Demonstrating a Multi-drug Resistant Mycobacterium tuberculosis Amplification Microarray

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Published on: April 25, 2014

Identification of Mycobacterium Species by DNA Microarray Chip Method

Identification of Mycobacterium Species by DNA Microarray Chip Method

Published on: June 24, 2025

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

Area of Science:

Bioinformatics
Genomics
Microarray technology

Background:

High-throughput sequencing of pathogen genomes necessitates methods for simultaneous analysis of multiple genomes.
Identifying common and unique genetic fingerprints across related pathogens is crucial for diagnostics and epidemiology.
Existing single-genome pipelines are insufficient for large-scale, multi-genome analysis.

Purpose of the Study:

To develop and present algorithmic enhancements to an existing single-genome pipeline for efficient, high-throughput design of microarray probes for multiple bacterial or viral genomes.
To enable the identification of both common and unique genetic fingerprints across groups of target genomes.
To reduce computation time for multi-genome probe design.

Main Methods:

Algorithmic enhancements to a single-genome pipeline.
Leveraging similarities in input genomes to narrow search to short, nonredundant regions.
Computation of a three-state hybridization matrix for expected probe-target hybridization.

Main Results:

The enhanced multiple-genome pipeline is nearly four-times faster than the single-genome pipeline for designing microarray probes.
Experimental testing with eight Burkholderia genomes showed less than 10% cross-hybridization with non-target genomes.
Over 65% of probes designed for Burkholderia mallei and B. pseudomallei strains successfully hybridized with an unsequenced B. pseudomallei strain.

Conclusions:

The enhanced pipeline significantly reduces runtime, enabling the design of fingerprints for tens or hundreds of related genomes in a single run.
The designed probes show potential utility in identifying unsequenced strains of B. mallei and B. pseudomallei.
This approach facilitates rapid and accurate pathogen identification and characterization.