Primer design using genetic algorithm

• Published in: Bioinformatics Vol. 20; no. 11; pp. 1710 - 1717
• Main Authors: Wu, Jain-Shing, Lee, Chungnan, Wu, Chien-Chang, Shiue, Yow-Ling
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 22.07.2004; Oxford Publishing Limited (England)
• Subjects: Algorithms; Base Sequence; Biological and medical sciences; Computer Simulation; DNA Primers - chemical synthesis; DNA Primers - chemistry; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Molecular Sequence Data; Polymerase Chain Reaction - methods; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Design; Primer; Genetics; Genetic algorithm; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth147

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.