EnsemPseU: Identifying Pseudouridine Sites With an Ensemble Approach
Yue Bi, Jin Dong, Cangzhi Jia
Abstract
Pseudouridine (Ψ) is the most prevalent RNA modification, which is formed from uridine through an isomerization reaction. With the increasing availability of genomic and proteomic samples, computer-aided pseudouridine-synthase-specific Ψ site recognition is becoming possible. In this paper, we propose an ensemble approach to identify pseudouridine sites, named EnsemPseU. First, five sequence-encoding strategies, namely, kmer, binary encoding, enhanced nucleic acid composition (ENAC), nucleotide chemical property (NCP), and nucleotide density (ND), were applied to extract sequence information. Then, chi-square feature selection was used to reduce the feature dimensionality and remove redundant information. Finally, an ensemble algorithm integrating support vector machine (SVM), extreme gradient boosting (XGBoost), naïve Bayes (NB), k-nearest neighbor (KNN), and random forest (RF) was used to build our prediction model. Upon testing, the results showed that the accuracy improved 5.3% for H. sapiens, 6.09% for S. cerevisiae, and 5.55% for M. musculus after chi-square feature selection. Moreover, upon evaluation via 10-fold cross-validation and an independent test, our proposed model EnsemPseU outperformed the other best existing model. The source code and data sets are available at https://github.com/biyue1026/EnsemPseU.