Non-Unique oligonucleotide probe selection heuristics
type: CreativeWork
description: The non-unique probe selection problem consists of selecting both unique and nonunique oligonucleotide probes for oligonucleotide microarrays, which are widely used tools to identify viruses or bacteria in biological samples. The non-unique probes, designed to hybridize to at least one target, are used as alternatives when the design of unique probes is particularly difficult for the closely related target genes. The goal of the non-unique probe selection problem is to determine a smallest set of probes able to identify all targets present in a biological sample. This problem is known to be NP-hard. In this thesis, several novel heuristics are presented based on greedy strategy, genetic algorithms and evolutionary strategy respectively for the minimization problem arisen from the non-unique probe selection using the best-known ILP formulation. Experiment results show that our methods are capable of reducing the number of probes required over the state-of-the-art methods.
abstract: The non-unique probe selection problem consists of selecting both unique and nonunique oligonucleotide probes for oligonucleotide microarrays, which are widely used tools to identify viruses or bacteria in biological samples. The non-unique probes, designed to hybridize to at least one target, are used as alternatives when the design of unique probes is particularly difficult for the closely related target genes. The goal of the non-unique probe selection problem is to determine a smallest set of probes able to identify all targets present in a biological sample. This problem is known to be NP-hard. In this thesis, several novel heuristics are presented based on greedy strategy, genetic algorithms and evolutionary strategy respectively for the minimization problem arisen from the non-unique probe selection using the best-known ILP formulation. Experiment results show that our methods are capable of reducing the number of probes required over the state-of-the-art methods.
author: Wang, Lili
language: en_CA
license: http://creativecommons.org/licenses/by-nc-nd/4.0/
date published: 2008-01-01
date modified: 2026-07-27T22:04:47Z
provider: University of Windsor
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Windsor

PropertyValue
property ID: Handle
value: https://hdl.handle.net/20.500.14776/8890