DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species

Abstract

Abstract Motivation DNA N4-methylcytosine (4mC) is a crucial epigenetic modification. However, the knowledge about its biological functions is limited. Effective and accurate identification of 4mC sites will be helpful to reveal its biological functions and mechanisms. Since experimental methods are cost and ineffective, a number of machine learning-based approaches have been proposed to detect 4mC sites. Although these methods yielded acceptable accuracy, there is still room for the improvement of the prediction performance and the stability of existing methods in practical applications. Results In this work, we first systematically assessed the existing methods based on an independent dataset. And then, we proposed DNA4mC-LIP, a linear integration method by combining existing predictors to identify 4mC sites in multiple species. The results obtained from independent dataset demonstrated that DNA4mC-LIP outperformed existing methods for identifying 4mC sites. To facilitate the scientific community, a web server for DNA4mC-LIP was developed. We anticipated that DNA4mC-LIP could serve as a powerful computational technique for identifying 4mC sites and facilitate the interpretation of 4mC mechanism. Availability and implementation http://i.uestc.edu.cn/DNA4mC-LIP/. Contact hlin@uestc.edu.cn or hj@uestc.edu.cn or chenweiimu@gmail.com Supplementary information Supplementary data are available at Bioinformatics online.