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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Primer design using genetic algorithm

Jain-Shing Wu 1,*, Chungnan Lee 1, Chien-Chang Wu 3 and Yow-Ling Shiue 2

1 Department of Computer Science and Engineering and 2 Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan and 3 Department of Food Engineering, Da-Yeh University, Taiwan

Received on September 18, 2003; revised on December 12, 2003; accepted on January 19, 2004
Advance Access Publication February 26, 2004

Motivation: Before performing a polymerase chain reaction experiment, a pair of primers to clip the target DNA subsequence is required. However, this is a tedious task as too many constraints need to be satisfied. Various kinds of approaches for designing a primer have been proposed in the last few decades, but most of them do not have restriction sites on the designed primers and do not satisfy the specificity constraint.

Results: The proposed algorithm imitates nature's process of evolution and genetic operations on chromosomes in order to achieve optimal solutions, and is a best fit for DNA behavior. Experimental results indicate that the proposed algorithm can find a pair of primers that not only obeys the design properties but also has a specific restriction site and specificity. Gel electrophoresis verifies that the proposed method really can clip out the target sequence.

Availability: A public version of the software is available on request from the authors.

Contact: wujs{at}mail.cse.nsysu.edu.tw

* To whom correspondence should be addressed.


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