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. 2007 Jun 1;30(2):249–268. doi: 10.1007/s00291-007-0089-0

A LAD-based method for selecting short oligo probes for genotyping applications

Kwangsoo Kim 1, Hong Seo Ryoo 1,✉
PMCID: PMC7080176  PMID: 32214570

Abstract

Specializing a general framework of logical analysis of data for efficiently handling large-scale genomic data, we develop in this paper a probe design method for selecting short oligo probes for genotyping applications. When tested on genomic sequences obtained from the National Center of Biotechnology Information 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.

Keywords: Oligo probes, Microarrays, LAD, Set covering, Classification, Optimization, SARS, AI

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