Selecting Genotyping Oligo Probes Via Logical Analysis of Data

Authors:
Kwangsoo Kim;Hong Seo Ryoo
Affiliations:
Division of Information Management Engineering, Korea University, 1, 5-Ka, Anam-Dong, Seongbuk-Ku, Seoul, 136-713, Korea;Division of Information Management Engineering, Korea University, 1, 5-Ka, Anam-Dong, Seongbuk-Ku, Seoul, 136-713, Korea
Venue:
CAI '07 Proceedings of the 20th conference of the Canadian Society for Computational Studies of Intelligence on Advances in Artificial Intelligence
Year:
2007

Citing 5
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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 silicoexperimental 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.