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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...
Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Performing Custom MicroRNA Microarray Experiments
07:04

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Published on: October 28, 2011

Microarray oligonucleotide probe designer (MOPeD): A web service.

Viren C Patel1, Kajari Mondal, Amol Carl Shetty

  • 1Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.

Open Access Bioinformatics
|March 8, 2011
PubMed
Summary
This summary is machine-generated.

Designing custom genomic selection microarrays is challenging. MOPeD (Microarray Oligonucleotide Probe Designer) software automates this process, improving genomic variation studies in complex genomes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Genomic selection methods utilize high-density oligonucleotide microarrays and next-generation DNA sequencing.
  • Characterizing genomic variation in complex eukaryotic genomes presents challenges in selecting appropriate oligonucleotide probes.

Purpose of the Study:

  • To develop an automated software solution for designing custom genomic selection microarrays.
  • To provide researchers with a tool for optimizing microarray design for specific genomic regions.

Main Methods:

  • Developed MOPeD (Microarray Oligonucleotide Probe Designer), a web-based software package.
  • Incorporated design parameters such as probe sequence uniqueness, melting temperature, hairpin formation, and single nucleotide polymorphisms.
  • Generated probe databases for human, mouse, and rhesus macaque genomes.

Main Results:

  • MOPeD-designed microarrays showed superior performance in human X chromosome exome sequencing compared to proprietary algorithms.
  • Experimental validation in mouse identified known mutations in targeted genomic regions.
  • Successfully designed and validated microarrays for human and mouse genomic studies.

Conclusions:

  • The open-source MOPeD software is a valuable resource for sequence-based studies of complex eukaryotic genomes.
  • Automated probe design enhances the efficiency and accuracy of genomic selection microarray development.
  • MOPeD facilitates custom microarray design for diverse research applications in genomics.