Primer design using genetic algorithm.

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.