A hybridization model for tiling array analysis

Tiling array is one type production of Affymetrix short oligonucleotide microarrays to map transcriptional factor binding sites (TFBS) at a high resolution. In order to estimate the quantity of target sequences of probes, we model the binding behavior between probes and DNA sequences at molecular interaction level and term it hybridization model for tiling array analysis (HMT). In our model, the binding behavior is affected by two main factors: the concentration of DNA fragments and the binding affinity of one probe with its target and off-target sequences. HMT mainly models the influence of binding affinity and gains the relative short DNA fragment abundance effectively. Results of comparison with another popular method suggest that HMT characterizes the hybridization mechanism of tiling array significantly. Another advantage of our model is that it is based on only one array and therefore can be easily extended to multiple arrays as well as other oligonucleotide array platforms.