DeepM6ASeq: Prediction and characterization of m6A-containing sequences using deep learning

Yiqian Zhang, Michiaki Hamada*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

80 Citations (Scopus)


Background: N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As a type of post-transcriptional methylation, m6A plays an important role in diverse RNA activities such as alternative splicing, an interplay with microRNAs and translation efficiency. Although existing tools can predict m6A at single-base resolution, it is still challenging to extract the biological information surrounding m6A sites. Results: We implemented a deep learning framework, named DeepM6ASeq, to predict m6A-containing sequences and characterize surrounding biological features based on miCLIP-Seq data, which detects m6A sites at single-base resolution. DeepM6ASeq showed better performance as compared to other machine learning classifiers. Moreover, an independent test on m6A-Seq data, which identifies m6A-containing genomic regions, revealed that our model is competitive in predicting m6A-containing sequences. The learned motifs from DeepM6ASeq correspond to known m6A readers. Notably, DeepM6ASeq also identifies a newly recognized m6A reader: FMR1. Besides, we found that a saliency map in the deep learning model could be utilized to visualize locations of m6A sites. Conculsion: We developed a deep-learning-based framework to predict and characterize m6A-containing sequences and hope to help investigators to gain more insights for m6A research. The source code is available at

Original languageEnglish
Article number524
JournalBMC Bioinformatics
Publication statusPublished - 2018 Dec 31


  • Deep learning
  • N6-methyladenosine
  • RNA modification

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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