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Bioinformatics Advance Access originally published online on October 25, 2005
Bioinformatics 2005 21(24):4330-4337; doi:10.1093/bioinformatics/bti730
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org
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Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens

Yu-Cheng Huang 1,{dagger}, Chun-Fan Chang 3,{dagger}, Chen-hsiung Chan 1, Tze-Jung Yeh 1,2, Ya-Chun Chang 2, Chaur-Chin Chen 4 and Cheng-Yan Kao 1,5,*

1Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University Taipei, Taiwan
2Department of Plant Pathology and Microbiology, National Taiwan University Taipei, Taiwan
3Breed-Use-Special Laboratory, Center of Agriculture Hierarchical Utilization, Graduate Institute of Biotechnology, Chinese Culture University Taipei, Taiwan
4Department of Computer Science, National Tsing-Hua University Hsinchu, Taiwan
5Institute for Information Industry Taipei, Taiwan

*To whom correspondence should be addressed.

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.

Results: The proposed PDA-MS/UniQ method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/probes designed with our integrated PDA-MS/UniQ method.

Contact: cykao{at}csie.ntu.edu.tw

Supplementary information: http://www.csie.ntu.edu.tw/~cykao/pda/

Received on May 27, 2005; revised on October 14, 2005; accepted on October 18, 2005

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