Multiplex PCR primer design for gene family using genetic algorithm
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Computational Biology and Chemistry
Fuzzy adaptive particle swarm optimization for a specific primer design problem
FUZZ-IEEE'09 Proceedings of the 18th international conference on Fuzzy Systems
Mutagenic Primer Design for Mismatch PCR-RFLP SNP Genotyping Using a Genetic Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
| Hi-index | 3.84 |
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.