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Nucleic Acids Research, 2003, Vol. 31, No. 19 5576-5581
© 2003 Oxford University Press

Genome-scale design of PCR primers and long oligomers for DNA microarrays

Stefan A. Haas*, Marc Hild1, Anthony P. H. Wright2,3, Torsten Hain4, Driss Talibi5 and Martin Vingron

Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestraße 73, D-14195 Berlin, Germany, 1 Center for Molecular Biology Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany, 2 Natural Sciences Section, Södertörns University College, S-141 89 Huddinge, Sweden, 3 Department of Biosciences, Karolinska Institute, Novum, S-141 57, Stockholm, Sweden, 4 Department of Medical Microbiology, Justus-Liebig University School of Medicine, Frankfurter Straße 107, 35392 Giessen, Germany and 5 Eurogentec SA, Parc Scientifique du Sart Tilman, 4102 Seraing, Belgium

*To whom correspondence should be addressed. Tel: +49 30 8413 1164; Fax: +49 30 8413 1152; Email: haas{at}molgen.mpg.de

During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40–70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21 306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.


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