An Optimization Method of Primer Design Based on Attention-BiLSTM

In this paper, we propose a method to predict the success of primer amplification based on the relationship existing between the sequence of primer and template, which can optimize the primer design and select the primer with better amplification from the candidate primer set. The double-stranded structure between primer and template nucleotide sequences is represented here by a number of words, each consisting of five characters that form sentences, as the dataset for the experiment, which is learned using an attention-based mechanism of bidirectional long short-term memory neural network model (Attention-BiLSTM), and then predicts primer amplification. The model predicted the results of polymerase chain reaction (PCR) involving specific primers and specific DNA templates with 82% accuracy, an improvement of about 2% over the performance of the LSTM with more stable value. These results show that the model can be used to effectively predict the results of PCR. This is the first paper to optimize primer design by screening the candidate primer set with a neural network model.