Implementation of logical analysis of data for oligo probe selection

In Yong Jang, Kwangsoo Kim, Hong Seo Ryoo

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.

Original languageEnglish
Title of host publicationOptimization in Medicine and Biology
PublisherTaylor and Francis
Pages415-438
Number of pages24
ISBN (Electronic)9780849305696
DOIs
Publication statusPublished - 2008 Jan 1

ASJC Scopus subject areas

  • Economics, Econometrics and Finance(all)
  • Business, Management and Accounting(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Engineering(all)

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