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Selecting Genotyping Oligo Probes Via Logical Analysis of Data

  • Kwangsoo Kim
  • Hong Seo Ryoo
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4509)

Abstract

Based on the general framework of logical analysis of data, we develop a probe design method for selecting short oligo probes for genotyping applications in this paper. When extensively tested on genomic sequences downloaded from the Lost Alamos National Laboratory and the National Center of Biotechnology Information websites in various monospecific and polyspecific in silico experimental settings, the proposed probe design method selected a small number of oligo probes of length 7 or 8 nucleotides that perfectly classified all unseen testing sequences. These results well illustrate the utility of the proposed method in genotyping applications.

Keywords

oligo probes microarrays LAD set covering learning theory optimization viral pathogens 

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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Kwangsoo Kim
    • 1
  • Hong Seo Ryoo
    • 1
  1. 1.Division of Information Management Engineering, Korea University, 1, 5-Ka, Anam-Dong, Seongbuk-Ku, Seoul, 136-713Korea

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