DPred_3S: identifying dihydrouridine (D) modification on three species epitranscriptome based on multiple sequence-derived features.
 Introduction:  Dihydrouridine (D) is a conserved modification of tRNA among all three life domains. D modification enhances the flexibility of a single nucleotide base in the spatial structure and is disease- and evolution-associated. Recent studies have also suggested the presence of dihydrouridine on mRNA.  Methods:  To identify D in epitranscriptome, we provided a prediction framework named "DPred_3S" based on the machine learning approach for three species D epitranscriptome, which used epitranscriptome sequencing data as training data for the first time.  Results:  The optimal features were evaluated by the F-score and integration of different features; our model achieved area under the receiver operating characteristic curve (AUROC) scores 0.955, 0.946, and 0.905 for  Saccharomyces cerevisiae ,  Escherichia coli , and  Schizosaccharomyces pombe , respectively. The performances of different machine learning algorithms were also compared in this study.  Discussion:  The high performances of our model suggest the D sites can be distinguished based on their surrounding sequence, but the lower performance of cross-species prediction may be limited by technique preferences.
Ren J, Chen X, Zhang Z, Shi H, Wu S