Primer design using genetic algorithm.
BACKGROUND
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.


BACKGROUND
A public version of the software is available on request from the authors.
Wu
Jain-Shing
JS
Department of Computer Science and Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan. wujs@mail.cse.nsysu.edu
Lee
Chungnan
C
Wu
Chien-Chang
CC
Shiue
Yow-Ling
YL
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D017931:DNA Primers / Q000138:chemical synthesis / Q000737:chemistry*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D017931:DNA Primers