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Nucleic Acids Research 2004 32(17):e133; doi:10.1093/nar/gnh127
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Published online 29 September 2004

Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved

Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays

Paul M. K. Gordon and Christoph W. Sensen*

Faculty of Medicine, Department of Biochemistry and Molecular Biology, Sun Center of Excellence for Visual Genomics, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada

* To whom correspondence should be addressed. Tel: +1 403 220 4301; Fax: +1 403 210 9538; Email: csensen{at}ucalgary.ca

Received August 11, 2004; Accepted August 20, 2004

We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted oligomers. It incorporates a novel use of position-specific scoring matrices, for the sensitive and specific identification of secondary binding sites anywhere in the target sequence. Using accelerated hardware is faster and more efficient than the traditional pairwise alignments used in most oligo-design software. Osprey consists of a module for target site selection based on user input, novel utilities for dealing with problematic sequences such as repeats, and a common code base for the identification of optimal oligonucleotides from the target list. Overall, these improvements provide a program that, without major increases in run time, reflects current DNA thermodynamics models, improves specificity and reduces the user's data preprocessing and parameterization requirements. Using a TimeLogicTM hardware accelerator, we report up to 50-fold reduction in search time versus a linear search strategy. Target sites may be derived from computer analysis of DNA sequence assemblies in the case of sequencing efforts, or genome or EST analysis in the case of microarray development in both prokaryotes and eukaryotes.


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