iRNAD: a computational tool for identifying D modification sites in RNA sequence

Abstract

Motivation: Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA.

Results: We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model.

Availability and implementation: A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.