Classification method for microarray probe selection using sequence, thermodynamics and secondary structure parameters

Probe design is the most important step for any microarray based assay. Accurate and efficient probe design and selection for the target sequence is critical in generating reliable and useful results. Several different approaches for probe design are reported in literature and an increasing number of bioinformatics tools are available for the same. However, based on the reported low accuracy, determining the hybridization efficiency of the probes is still a big computational challenge. Present study deals with the extraction of various novel features related to sequence composition, thermodynamics and secondary structure that may be essential for designing good probes. A feature selection method has been used to assess the relative importance of all these features. In this paper, we validate the importance of various features currently used for designing an oligonucleotide probe. Finally, a classification methodology is presented that can be used to predict the hybridization quality of a probe.