Abstract
MotivationThe biological function of N 6-methyladenine DNA (6mA) in plants is largely unknown. Rice is one of the most important crops worldwide and is a model species for molecular and genetic studies. There are few methods for 6mA site recognition in the rice genome, and an effective computational method is needed.ResultsIn this paper, we propose a new computational method called 6mA-Pred to identify 6mA sites in the rice genome. 6mA-Pred employs a feature fusion method to combine advantageous features from other methods and thus obtain a new feature to identify 6mA sites. This method achieved an accuracy of 87.27% in the identification of 6mA sites with 10-fold cross-validation and achieved an accuracy of 85.6% in independent test sets.
Highlights
DNA methylation plays crucial roles in many biological functions, and methylated DNA carries important epigenetic information
We propose a feature fusion-based method to identify 6mA sites in the rice genome, in which nucleotide chemical properties, binary encoding, KMER, and Markov features are used to formulate DNA sequences
Our method, which is based on feature fusion, achieved better results than these previous methods in identifying 6mA sites in the rice genome
Summary
DNA methylation plays crucial roles in many biological functions, and methylated DNA carries important epigenetic information. The modification of DNA methylation is a heavily researched topic in epigenetic research (Liu et al, 2016). With the rapid development of sequencing technology, a new type of DNA methylation modification, DNA-6mA methylation, has been identified and has become a heavily researched subject in the field of epigenetics (Xiao et al, 2018). N6-methyladenine DNA (6mA) modification is the most prevalent type of DNA modification in prokaryotes. This modification plays important roles in DNA mismatch repair, chromosome replication, cell defense, cell cycle regulation, and transcription (Xu et al, 2017; He et al, 2019). This modification plays important roles in DNA mismatch repair, chromosome replication, cell defense, cell cycle regulation, and transcription (Xu et al, 2017; He et al, 2019). 6mA shows similar properties in eukaryotes and prokaryotes (Hao et al, 2019)
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