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Open Access Methodology article

Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy

Guangan Hu1, Manuel Llinás2, Jingguang Li3, Peter Rainer Preiser1 and Zbynek Bozdech1*

Author Affiliations

1 School of Biological Sciences, Nanyang Technological University, No. 60 Nanyang Drive, 637551, Singapore

2 Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University 246 Carl Icahn Laboratory, Princeton NJ 08544, USA

3 Department of Pathology & Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore

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BMC Bioinformatics 2007, 8:350  doi:10.1186/1471-2105-8-350

Published: 19 September 2007

Abstract

Background

The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonucleotide element that represents each genetic locus/gene in the genome and is unique, devoid of internal structures and repetitive sequences and its Tm is uniform with all other elements on the microarray. Currently, all of the publicly available programs for DNA long oligonucleotide microarray selection utilize various combinations of cutoffs in which each parameter (uniqueness, Tm, and secondary structure) is evaluated and filtered individually. The use of the cutoffs can, however, lead to information loss and to selection of suboptimal oligonucleotides, especially for genomes with extreme distribution of the GC content, a large proportion of repetitive sequences or the presence of large gene families with highly homologous members.

Results

Here we present the program OligoRankPick which is using a weighted rank-based strategy to select microarray oligonucleotide elements via an integer weighted linear function. This approach optimizes the selection criteria (weight score) for each gene individually, accommodating variable properties of the DNA sequence along the genome. The designed algorithm was tested using three microbial genomes Escherichia coli, Saccharomyces cerevisiae and the human malaria parasite species Plasmodium falciparum. In comparison to other published algorithms OligoRankPick provides significant improvements in oligonucleotide design for all three genomes with the most significant improvements observed in the microarray design for P. falciparum whose genome is characterized by large fluctuations of GC content, and abundant gene duplications.

Conclusion

OligoRankPick is an efficient tool for the design of long oligonucleotide DNA microarrays which does not rely on direct oligonucleotide exclusion by parameter cutoffs but instead optimizes all parameters in context of each other. The weighted rank-sum strategy utilized by this algorithm provides high flexibility of oligonucleotide selection which accommodates extreme variability of DNA sequence properties along genomes of many organisms.