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Bioinformatics Advance Access published online on August 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti001
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 29, 2004
Revised August 19, 2004
Accepted August 20, 2004

Article

Dual-genome primer design for construction of DNA microarrays

Anders Andersson 1, Rolf Bernander 2, Peter Nilsson 3*

1 Department of Biotechnology, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden; Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden
2 Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden
3 Department of Biotechnology, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden

* To whom correspondence should be addressed. E-mail: peter.nilsson{at}biotech.kth.se.


  Abstract

Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information.

Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR reaction can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared between 705 pairs of genes, and single primers were shared between 1184 pairs of genes, resulting in savings of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

Availability: The software is freely available at http://www.biotech.kth.se/molbio/microarray/ (During review process only available at ftp://biobase.biotech.kth.se under dualprime, username: microarray, password: array1050kth).


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