Bioinformatics Advance Access published online on October 25, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti730
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1 Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, 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 to 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. Supplementary Material: http://www.csie.ntu.edu.tw/~cykao/pda/.
Received May 27, 2005
Revised October 14, 2005
Accepted October 18, 2005
Article
Integrated minimum-set primers and unique probes design algorithms for differential detection on symptom-related pathogens
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2 Breed-Use-Special Laboratory, Center of Agriculture Hierarchical Utilization, Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
3 Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan; Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
4 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
5 Department of Computer Science, National Tsing-Hua University, Hsinchu, Taiwan
6 Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan; Institute for Information Industry, Taipei, Taiwan
Cheng-Yan Kao, E-mail: cykao{at}csie.ntu.edu.tw
Abstract Equal contributions.
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