Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens

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Please use this identifier to cite or link to this item: https://irlib.pccu.edu.tw/handle/987654321/2433

Title:	Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens
Authors:	Huang, Y.C.;Chang, C.F.;Chan, C.H.;Yeh, T.J.;Chang, Y.C.;Chen, C.C.;Kao, C.Y.
Contributors:	生物科技研究所
Date:	2005
Issue Date:	2009-10-30 15:25:24 (UTC+8)
Abstract:	Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP.
Relation:	BIOINFORMATICS v.21 n.24 Pages: 4330-4337
Appears in Collections:	[Graduate Institute of Biotechnology ] journal articles

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