A LAD-based method for selecting short oligo probes for genotyping applications

Kwangsoo Kim; Hong Seo Ryoo

doi:10.1007/s00291-007-0089-0

A LAD-based method for selecting short oligo probes for genotyping applications

Kwangsoo Kim, Hong Seo Ryoo

Research output: Contribution to journal › Article › peer-review

16 Citations (Scopus)

Abstract

Specializing a general framework of logical analysis of data for efficiently handling large-scale genomic data, we develop in this paper a probe design method for selecting short oligo probes for genotyping applications. When tested on genomic sequences obtained from the National Center of Biotechnology Information 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 language	English
Pages (from-to)	249-268
Number of pages	20
Journal	OR Spectrum
Volume	30
Issue number	2
DOIs	https://doi.org/10.1007/s00291-007-0089-0
Publication status	Published - 2008 Apr

Keywords

AI
Classification
LAD
Microarrays
Oligo probes
Optimization
SARS
Set covering

ASJC Scopus subject areas

Management Science and Operations Research

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10.1007/s00291-007-0089-0

Cite this

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title = "A LAD-based method for selecting short oligo probes for genotyping applications",

abstract = "Specializing a general framework of logical analysis of data for efficiently handling large-scale genomic data, we develop in this paper a probe design method for selecting short oligo probes for genotyping applications. When tested on genomic sequences obtained from the National Center of Biotechnology Information 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.",

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AB - Specializing a general framework of logical analysis of data for efficiently handling large-scale genomic data, we develop in this paper a probe design method for selecting short oligo probes for genotyping applications. When tested on genomic sequences obtained from the National Center of Biotechnology Information 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.

KW - AI

KW - Classification

KW - LAD

KW - Microarrays

KW - Oligo probes

KW - Optimization

KW - SARS

KW - Set covering

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ER -

A LAD-based method for selecting short oligo probes for genotyping applications

Abstract

Keywords

ASJC Scopus subject areas

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