Computational Sequence Design Techniques for DNA Microarray Technologies

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Author(s): Dan Tulpan (National Research Council of Canada, Canada), Athos Ghiggi (University of Lugano (USI), Switzerland)and Roberto Montemanni (Istituto Dalle Molle di Studi sull’Intelligenza Artificiale (IDSIA), Switzerland)
Copyright: 2012
Pages: 35
Source title: Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances
Source Author(s)/Editor(s): Paola Lecca (The Microsoft Research – University of Trento, Centre for Computational and Systems Biology, Italy), Dan Tulpan (National Research Council of Canada, Canada)and Kanagasabai Rajaraman (Institute for Infocomm Research, Singapore)
DOI: 10.4018/978-1-61350-435-2.ch003

Keywords: Bioinformatics / Medical Information Science Reference / Medicine & Healthcare

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Abstract

In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.

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