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Related Concept Videos

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 16, 2026

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
09:13

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

Published on: January 13, 2016

Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays.

Hedda Høvik1, Tsute Chen

  • 1Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.

BMC Bioinformatics
|February 11, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a computational pipeline for designing microbial transcriptome tiling probe sets. The pipeline ensures optimal probe selection for high-density arrays, enabling comprehensive genomic studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • High-density oligonucleotide microarrays are suitable for microbial transcriptome analysis using tiling probe designs.
  • A comprehensive computational pipeline is presented for designing these tiling probe sets.

Purpose of the Study:

  • To develop and describe a computational pipeline for designing microbial transcriptome tiling probe sets.
  • To enable efficient and comprehensive transcriptome profiling of microbial genomes.

Main Methods:

  • The pipeline identifies all possible probe sequences from both strands of microbial DNA, adjusting lengths for synthesis and isothermality.
  • Probes are selected in sequential and gap-filling stages based on uniqueness, self-annealing, melting temperature, length, and position.
  • Evaluates global and local probe properties for dynamic, even genome distribution.

Main Results:

  • Identifies all potential probe sequences from microbial genomes (chromosomes and plasmids).
  • Selects optimal probes using a two-stage process (sequential and gap-filling) based on five quality criteria.
  • Ensures probes are unique, stable, and evenly distributed across the genome.

Conclusions:

  • The pipeline designs an exact number of non-redundant probes for any microarray platform.
  • Enables dynamic and even probe distribution along the target genome.
  • Applicable to microbial comparative genomics, ChIP-chip, gene expression, and transcriptome studies.