IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011. In press.
For designing oligonucleotide tiling arrays popular current methods still rely on simple criteria like Hamming distance or longest common factors, neglecting base stacking effects which strongly contribute to binding energies. Consequently, probes are often prone to cross-hybridization which reduces the signal-to-noise ratio and complicates downstream analysis. We propose the first computationally efficient method using hybridization-energy to identify specific oligonucleotide probes. Our Cross Hybridization Potential (CHP) is computed with a Nearest Neighbor Alignment, which efficiently estimates a lower bound for the Gibbs free energy of the duplex formed by two DNA sequences of bounded length. It is derived from our simplified reformulation of t-gap insertion-deletion-like metrics. The computations are accelerated by a filter using weighted ungapped q-grams. The computation of the CHP is implemented in our software OSProbes, available under the GPL, which computes sets of viable probe candidates. The user can choose a tradeoff between running time and quality of probes selected. We obtain very favorable results in comparison with prior approaches with respect to specificity and sensitivity for cross-hybridization and genome coverage with high-specificity probes. The combination of OSProbes and our Tileomatic method yields globally optimal tiling arrays, balancing probe distance, hybridization conditions and uniqueness of hybridization.