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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages86-97
Number of pages12
Volume4509 LNAI
Publication statusPublished - 2007 Dec 24
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)03029743
ISSN (Electronic)16113349

Other

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

Fingerprint

Probe
Design Method
Information Centers
Biotechnology
Computer Simulation
Nucleotides
Genomics
Websites
Testing

Keywords

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

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Kim, K., & Ryoo, H. S. (2007). Selecting genotyping oligo probes via logical analysis of data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4509 LNAI, pp. 86-97). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4509 LNAI).

Selecting genotyping oligo probes via logical analysis of data. / Kim, Kwangsoo; Ryoo, Hong Seo.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4509 LNAI 2007. p. 86-97 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4509 LNAI).

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

Kim, K & Ryoo, HS 2007, Selecting genotyping oligo probes via logical analysis of data. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 4509 LNAI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4509 LNAI, pp. 86-97, 20th Conference of the Canadian Society for Computational Studies of Intelligence, CSCSI, Canadian AI 2007, Montreal, Canada, 07/5/28.
Kim K, Ryoo HS. Selecting genotyping oligo probes via logical analysis of data. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4509 LNAI. 2007. p. 86-97. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Kim, Kwangsoo ; Ryoo, Hong Seo. / Selecting genotyping oligo probes via logical analysis of data. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4509 LNAI 2007. pp. 86-97 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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