title: Estimation of teaching-learning-based optimization primer design using regression analysis for different melting temperature calculations.
abstract: Primers plays important role in polymerase chain reaction (PCR) experiments, thus it is necessary to select characteristic primers. Unfortunately, manual primer design manners are time-consuming and easy to get human negligence because many PCR constraints must be considered simultaneously. Automatic programs for primer design were developed urgently. In this study, the teaching-learning-based optimization (TLBO), a robust and free of algorithm-specific parameters method, is applied to screen primers conformed primer constraints. The optimal primer frequency (OPF) based on three known melting temperature formulas is estimated by 500 runs for primer design in each different number of generations. We selected optimal primers from fifty random nucleotide sequences of Homo sapiens at NCBI. The results indicate that the SantaLucia's formula is better coupled with the method to get higher optimal primer frequency and shorter CPU-time than the Wallace's formula and the Bolton and McCarthy's formula. Through the regression analysis, we also find the generations are significantly associated with the optimal primer frequency. The results are helpful for developing the novel TLBO-based computational method to design feasible primers.
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
mesh_terms: D000465:Algorithms; D000704:Analysis of Variance; D001185:Artificial Intelligence; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D017931:DNA Primers; D006801:Humans; D016133:Polymerase Chain Reaction; D012044:Regression Analysis; D044366:Transition Temperature
chemical_list: D017931:DNA Primers; D004247:DNA