Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Probe selection for DNA microarrays using OligoWiz.

Rasmus Wernersson1, Agnieszka S Juncker, Henrik Bjørn Nielsen

  • 1Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby 2800, Denmark. raz@cbs.dtu.dk

Nature Protocols
|November 17, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Molecular maps of diseases from omics data and network embeddings.

NPJ systems biology and applications·2026
Same author

Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.

Clinical nutrition (Edinburgh, Scotland)·2026
Same author

The HUNT study identifies host genetic factors reproducibly associated with human gut microbiota composition.

Nature genetics·2026
Same author

Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization.

Nature microbiology·2026
Same author

Correction: New insights into the molecular biology of Alzheimer's-like cerebral amyloidosis achieved through multi-omics approaches.

PloS one·2025
Same author

DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.

mSystems·2025
Same journal

iMUT-seq mapping of DSB-induced mutations with high sensitivity at single-nucleotide resolution.

Nature protocols·2026
Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026
Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026
Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026
Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026
Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026
See all related articles

This study introduces OligoWiz, a web-based tool for selecting DNA probes for DNA microarrays. OligoWiz simplifies probe design, enabling efficient nucleotide abundance measurements and analysis of gene expression.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Accurate nucleotide abundance measurements via DNA microarrays depend on identifying suitable complementary DNA probes.
  • The selection of effective probes is a critical step in microarray design and analysis.

Purpose of the Study:

  • To present a protocol for selecting DNA probes for microarrays utilizing the OligoWiz application.
  • To provide a user-friendly and efficient method for designing DNA probes for various applications.

Main Methods:

  • Utilized the OligoWiz client-server application for probe selection.
  • Employed five weighted scores: cross-hybridization, deltaT(m), folding, position, and low-complexity.
  • Integrated sequence annotation using regular expressions for precise probe placement.

Related Experiment Videos

Main Results:

  • OligoWiz offers a detailed graphical interface and real-time user interaction.
  • The application leverages substantial computing power and extensive species databases.
  • A standard microarray probe selection for all yeast transcripts can be completed within one hour.

Conclusions:

  • The OligoWiz protocol facilitates efficient DNA probe selection for microarrays.
  • The protocol requires minimal computer expertise and is accessible via the internet.
  • This method streamlines the process of nucleotide abundance measurement and gene expression analysis.