Selecting genotyping oligo probes via logical analysis of data

Kwangsoo Kim, Hong Seo Ryoo

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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.

Original languageEnglish
Title of host publicationAdvances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings
PublisherSpringer Verlag
Pages86-97
Number of pages12
ISBN (Print)9783540726647
DOIs
Publication statusPublished - 2007
Event20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007 - Montreal, Canada
Duration: 2007 May 282007 May 30

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4509 LNAI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007
CountryCanada
CityMontreal
Period07/5/2807/5/30

Keywords

  • LAD
  • Learning theory
  • Microarrays
  • Oligo probes
  • Optimization
  • Set covering
  • Viral pathogens

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Fingerprint Dive into the research topics of 'Selecting genotyping oligo probes via logical analysis of data'. Together they form a unique fingerprint.

  • Cite this

    Kim, K., & Ryoo, H. S. (2007). Selecting genotyping oligo probes via logical analysis of data. In Advances in Artificial Intelligence - 20th Conference of the Canadian Society for Computational Studies of Intelligence, Canadian AI 2007, Proceedings (pp. 86-97). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4509 LNAI). Springer Verlag. https://doi.org/10.1007/978-3-540-72665-4_8