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Nucleic Acids Research, 2003, Vol. 31, No. 13 3491-3496
© 2003 Oxford University Press

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

Henrik Bjørn Nielsen*, Rasmus Wernersson and Steen Knudsen

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark

*To whom correspondence should be addressed. Tel: +45 45252489; Fax: +45 45931585; Email: hbjorn{at}cbs.dtu.dk

Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added to the program to extend the default parameters: homology, {Delta}Tm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/.


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