Signal peptides play an important role in guiding and transferring transmembrane proteins and secreted proteins. In recent years, with the explosive growth of protein sequences, computationally predicting signal peptides and their cleavage sites from protein sequences is highly desired. In this work, we present an improved approach, Signal-3L 3.0, for signal peptide recognition and cleavage-site prediction using a 3-layer hybrid method of integrating deep learning algorithms and window-based scoring. There are three main components in the Signal-3L 3.0 prediction engine: (1) a deep bidirectional long short-term memory (Bi-LSTM) network with a soft self-attention learns abstract features from sequences to determine whether a query protein contains a signal peptide; (2) the statistics propensity window-based cleavage site screening method is applied to generate the set of candidate cleavage sites; (3) the prediction of a conditional random field with a hybrid convolutional neural network (CNN) and Bi-LSTM is fused with the window-based score for identifying the final unique cleavage site. Experimental results on the benchmark datasets show that the new deep learning-driven Signal-3L 3.0 yields promising performance. The online server of Signal-3L 3.0 is available at http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/.

中文翻译：

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Signal-3L 3.0：通过将注意力深度学习与基于窗口的评分相结合来改进信号肽预测。

信号肽在引导和转移跨膜蛋白和分泌蛋白方面发挥着重要作用。近年来，随着蛋白质序列的爆炸式增长，非常需要计算预测蛋白质序列中的信号肽及其切割位点。在这项工作中，我们提出了一种改进的方法 Signal-3L 3.0，它使用集成深度学习算法和基于窗口的评分的 3 层混合方法进行信号肽识别和切割位点预测。Signal-3L 3.0 预测引擎中包含三个主要组件：(1) 具有软自注意力的深度双向长短期记忆 (Bi-LSTM) 网络从序列中学习抽象特征，以确定查询蛋白是否包含信号肽；(2)应用基于统计倾向窗的切割位点筛选方法生成候选切割位点集合；(3) 使用混合卷积神经网络 (CNN) 和 Bi-LSTM 对条件随机场的预测与基于窗口的分数融合，以识别最终的独特切割位点。基准数据集的实验结果表明，新的深度学习驱动的 Signal-3L 3.0 产生了可观的性能。Signal-3L 3.0 的在线服务器位于 http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/。基准数据集的实验结果表明，新的深度学习驱动的 Signal-3L 3.0 产生了可观的性能。Signal-3L 3.0 的在线服务器位于 http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/。基准数据集的实验结果表明，新的深度学习驱动的 Signal-3L 3.0 产生了可观的性能。Signal-3L 3.0 的在线服务器位于 http://www.csbio.sjtu.edu.cn/bioinf/Signal-3L/。