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Open Access Research article

BOND: Basic OligoNucleotide Design

Lucian Ilie1*, Hamid Mohamadi2, Geoffrey Brian Golding3 and William F Smyth2

Author Affiliations

1 Department of Computer Science, University of Western Ontario, London, ON, N6A5B7, Canada

2 Department of Computing and Software, McMaster University, Hamilton, ON, L8S 4K1, Canada

3 Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada

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BMC Bioinformatics 2013, 14:69  doi:10.1186/1471-2105-14-69

Published: 27 February 2013



DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind only to the intended target, (ii) cover the highest possible number of genes, that is, all genes that allow such unique regions, and (iii) are computed fast. None of the existing programs meet all these criteria.


We introduce a new approach with our software program BOND (Basic OligoNucleotide Design). According to Kane’s criteria for oligo design, BOND computes highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. The same approach enables us to introduce also an evaluation procedure that correctly measures the quality of the oligonucleotides. Extensive comparison is performed to prove our claims. BOND is flexible, easy to use, requires no additional software, and is freely available for non-commercial use from webcite.


We provide an improved solution to the important problem of oligonucleotide design, including a thorough evaluation of oligo design programs. We hope BOND will become a useful tool for researchers in biological and medical sciences by making the microarray procedures faster and more accurate.

DNA oligonucleotide design; Microarray; Spaced seeds