2nd International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems

Research Article

A Model-Based Approach to the Non-Unique Oligonucleotide Probe Selection Problem

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  • @INPROCEEDINGS{10.4108/ICST.BIONETICS2007.2430,
        author={Lili Wang and Alioune Ngom},
        title={A Model-Based Approach to the Non-Unique Oligonucleotide Probe Selection Problem},
        proceedings={2nd International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems},
        proceedings_a={BIONETICS},
        year={2008},
        month={8},
        keywords={Hybridization  Microarray  Probabilistic model  Probe selection},
        doi={10.4108/ICST.BIONETICS2007.2430}
    }
    
  • Lili Wang
    Alioune Ngom
    Year: 2008
    A Model-Based Approach to the Non-Unique Oligonucleotide Probe Selection Problem
    BIONETICS
    ICST
    DOI: 10.4108/ICST.BIONETICS2007.2430
Lili Wang1,*, Alioune Ngom1,*
  • 1: School of Computer Science, University of Windsor 5115 Lambton Tower, 401 Sunset Avenue Windsor, N9B 3P4, Ontario, Canada 01-519-253-3000
*Contact email: wang111v@uwindsor.ca, angom@cs.uwindsor.ca

Abstract

In order to accurately measure the gene expression levels in oligonucleotide microarray experiments, it is crucial to design “unique”, highly specific and sensitive probes for the identification of biological agents such as genes in a sample. It is difficult to design unique probes for very closely related genes, such as the known strains of HIV genes. The “non-unique” probe selection problem consists of determining a set of probes, not necessarily unique, that can uniquely identify targets while containing a minimal number of probes. In this paper, we describe a simple model-based method to obtain a near minimal non-unique probe set. Preliminary experimental results are encouraging and at least comparable, if not better, to those obtained by two recently published methods.