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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...
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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Performing Custom MicroRNA Microarray Experiments
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Published on: October 28, 2011

In silico gene selection for custom oligonucleotide microarray design.

Conor W Sipe1, Vijay R Dondeti, Margaret S Saha

  • 1Department of Biology, College of William and Mary, Williamsburg, VA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|January 29, 2008
PubMed
Summary
This summary is machine-generated.

This study presents a Perl-based method for selecting oligonucleotide sequences to custom design microarrays. The approach ensures accurate sequence orientation, enabling robust custom microarray design for any organism with available sequence data.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Custom oligonucleotide microarrays require systematic selection of numerous sequences.
  • Public sequence databases may contain annotation inaccuracies, necessitating sequence verification.

Purpose of the Study:

  • To develop a method for efficiently and accurately selecting sequences for custom oligonucleotide microarray design.
  • To address concerns regarding sequence annotation accuracy in public databases.

Main Methods:

  • Utilized Perl scripts to query sequence databases using gene lists from existing microarrays.
  • Implemented a homologous sequence selection process with user-defined thresholds.
  • Developed a secondary script to verify sequence orientation using protein similarity from Unigene records.

Main Results:

  • A candidate gene database was populated with homologous sequences passing defined criteria.
  • The method allows for the design of microarrays for any organism with sequence data.
  • Discrepancies in sequence orientation were identified by comparing protein similarity data with assigned orientations.

Conclusions:

  • The presented method offers a versatile approach for custom microarray design.
  • Sequence orientation verification enhances the reliability of custom-designed microarrays.
  • This technique supports pathway-specific and process-specific microarray applications.