As a prevalent existing post-transcriptional modification of RNA, N6-methyladenosine (m6A) plays a crucial role in various biological processes. To better radically reveal its regulatory mechanism and provide new insights for drug design, the accurate identification of m6A sites in genome-wide is vital. As the traditional experimental methods are time-consuming and cost-prohibitive, it is necessary to design a more efficient computational method to detect the m6A sites. In this study, we propose a novel cross-species computational method DNN-m6A based on the deep neural network (DNN) to identify m6A sites in multiple tissues of human, mouse and rat. Firstly, binary encoding (BE), tri-nucleotide composition (TNC), enhanced nucleic acid composition (ENAC), K-spaced nucleotide pair frequencies (KSNPFs), nucleotide chemical property (NCP), pseudo dinucleotide composition (PseDNC), position-specific nucleotide propensity (PSNP) and position-specific dinucleotide propensity (PSDP) are employed to extract RNA sequence features which are subsequently fused to construct the initial feature vector set. Secondly, we use elastic net to eliminate redundant features while building the optimal feature subset. Finally, the hyper-parameters of DNN are tuned with Bayesian hyper-parameter optimization based on the selected feature subset. The five-fold cross-validation test on training datasets show that the proposed DNN-m6A method outperformed the state-of-the-art method for predicting m6A sites, with an accuracy (ACC) of 73.58–83.38% and an area under the curve (AUC) of 81.39–91.04%. Furthermore, the independent datasets achieved an ACC of 72.95–83.04% and an AUC of 80.79–91.09%, which shows an excellent generalization ability of our proposed method.

As one of the most prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays an essential role in the regulation of gene expression. Accurate identification of m7G sites in the transcriptome is invaluable for better revealing their potential functional mechanisms. Although high-throughput experimental methods can locate m7G sites precisely, they are overpriced and time-consuming. Hence, it is imperative to design an efficient computational method that can accurately identify the m7G sites. In this study, we propose a novel method via incorporating BERT-based multilingual model in bioinformatics to represent the information of RNA sequences. Firstly, we treat RNA sequences as natural sentences and then employ bidirectional encoder representations from transformers (BERT) model to transform them into fixed-length numerical matrices. Secondly, a feature selection scheme based on the elastic net method is constructed to eliminate redundant features and retain important features. Finally, the selected feature subset is input into a stacking ensemble classifier to predict m7G sites, and the hyperparameters of the classifier are tuned with tree-structured Parzen estimator (TPE) approach. By 10-fold cross-validation, the performance of BERT-m7G is measured with an ACC of 95.48% and an MCC of 0.9100. The experimental results indicate that the proposed method significantly outperforms state-of-the-art prediction methods in the identification of m7G modifications.

Succinylation is an important posttranslational modification of proteins, which plays a key role in protein conformation regulation and cellular function control. Many studies have shown that succinylation modification on protein lysine residue is closely related to the occurrence of many diseases. To understand the mechanism of succinylation profoundly, it is necessary to identify succinylation sites in proteins accurately. In this study, we develop a new model, IFS-LightGBM (BO), which utilizes the incremental feature selection (IFS) method, the LightGBM feature selection method, the Bayesian optimization algorithm, and the LightGBM classifier, to predict succinylation sites in proteins. Specifically, pseudo amino acid composition (PseAAC), position-specific scoring matrix (PSSM), disorder status, and Composition of -spaced Amino Acid Pairs (CKSAAP) are firstly employed to extract feature information. Then, utilizing the combination of the LightGBM feature selection method and the incremental feature selection (IFS) method selects the optimal feature subset for the LightGBM classifier. Finally, to increase prediction accuracy and reduce the computation load, the Bayesian optimization algorithm is used to optimize the parameters of the LightGBM classifier. The results reveal that the IFS-LightGBM (BO)-based prediction model performs better when it is evaluated by some common metrics, such as accuracy, recall, precision, Matthews Correlation Coefficient (MCC), and -measure.

Protein fold recognition contribute to comprehend the function of proteins, which is of great help to the gene therapy of diseases and the development of new drugs. Researchers have been working in this direction and have made considerable achievements, but challenges still exist on low sequence similarity datasets. In this study, we propose the ASFold-DNN framework for protein fold recognition research. Above all, four groups of evolutionary features are extracted from the primary structures of proteins, and a preliminary selection of variable parameter is made for two groups of features including ACC HMM and SXG HMM, respectively. Then several feature selection algorithms are selected for comparison and the best feature selection scheme is obtained by changing their internal threshold values. Finally, multiple hyper-parameters of Full Connected Neural Network are fully optimized to construct the best model. DD, EDD and TG datasets with low sequence similarities are chosen to evaluate the performance of the models constructed by the framework, and the final prediction accuracy are 85.28%, 95.00% and 88.84%, respectively. Furthermore, the ASTRAL186 and LE datasets are introduced to further verify the generalization ability of our proposed framework. Comprehensive experimental results prove that the ASFold-DNN framework is more prominent than the state-of-the-art studies on protein fold recognition. The source code and data of ASFold-DNN can be downloaded from https://github.com/Bioinformatics-Laboratory/project/tree/master/ASFold.

Understanding the tertiary structures of proteins is of great benefit to function in many aspects of human life. Protein fold recognition is a vital and salient means to know protein structure. Until now, researchers have successively proposed a variety of methods to realize protein fold recognition, but the novel and effective computational method is still needed to handle this problem with the continuous updating of protein structure databases. In this study, we develop a new protein structure dataset named AT and propose the PRFold-TNN model for protein fold recognition. Firstly, different types of feature extraction methods including AAC, HMM, HMM-Bigram and ACC are selected to extract corresponding features for protein sequences. Then an ensemble feature selection method based on PageRank algorithm integrating various tree-based algorithms is used to screen the fusion features. Ultimately, the classifier based on the Transformer model achieves the final prediction. Experiments show that the prediction accuracy is 86.27% on the AT dataset and 88.91% on the independent test set, indicating that the model can demonstrate superior performance and generalization ability in the problem of protein fold recognition. Furthermore, we also carry out research on the DD, EDD and TG benchmark datasets, and make them achieve prediction accuracy of 88.41%, 97.91% and 95.16%, which are at least 3.0%, 0.8% and 2.5% higher than those of the state-of-the-art methods. It can be concluded that the PRFold-TNN model is more prominent.