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In Journal of computational biology : a journal of computational molecular cell biology

Recently, a deep learning-based enhancing Position-Specific Scoring Matrix (PSSM) method (Bagging Multiple Sequence Alignment [MSA] Learning) Guo et al. has been proposed, and its effectiveness has been empirically proved. Program EPTool is the implementation of Bagging MSA Learning, which provides a complete training and evaluation workflow for the enhancing PSSM model. It is capable of handling different input data set and various computing algorithms to train the enhancing model, then eventually improve the PSSM quality for those proteins with insufficient homologous sequences. In addition, EPTool equips several convenient applications, such as PSSM features calculator, and PSSM features visualization. In this article, we propose designed EPTool and briefly introduce its functionalities and applications. The detailed accessible instructions are also provided.

Guo Yuzhi, Wu Jiaxiang, Ma Hehuan, Wang Sheng, Huang Junzhou


deep learning, enhancing PSSM, protein secondary structure prediction, unsupervised learning