PB-LKS: a python package for predicting phage–bacteria interaction through local K-mer strategy
Jingxuan Qiu, Wanchun Nie, Hao Ding, Jia Le Dai, Yiwen Wei, Dezhi Li, Yuxi Zhang, Junting Xie, Xinxin Tian, Nannan Wu, Tianyi Qiu
Abstract
Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship of phages across strain mutants. This has hindered the development of phage therapeutics based on the prediction of phage-bacteria relationships. In this paper, we present, PB-LKS, to predict the phage-bacteria interaction based on local K-mer strategy with higher performance and wider applicability. The utility of PB-LKS is rigorously validated through (i) large-scale historical screening, (ii) case study at the class level and (iii) in vitro simulation of bacterial antiphage resistance at the strain mutant level. The PB-LKS approach could outperform the current state-of-the-art methods and illustrate potential clinical utility in pre-optimized phage therapy design.