Implementation of Logical Analysis of Data for Oligo Probe Selection
Abstract Specializing a general framework of logical analysis of data for efﬁciently handling large-scale genomic data, we develop in this chapter a probe design method for selecting short oligo probes for genotyping applications. Extensively tested on genomic sequences obtained from the National Center of Biotechnology Information (NCBI) in various monospeciﬁc and polyspeciﬁc in silico experiments, the proposed probe design method was able to select a small number of oligo probes of length 7 or 8
nucleotides that perfectly classiﬁed all unseen testing sequences. These results demonstrate the efﬁcacy of the proposed probe design method and illustrate the usefulness and potential a well-designed optimization-based probe selection method has in genotyping applications.