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RBPsuite: RNA-protein binding sites prediction suite based on deep learning.

Xiaoyong Pan1, Yi Fang2, Xianfeng Li3

  • 1Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China. 2008xypan@sjtu.edu.cn.

BMC Genomics
|December 10, 2020
PubMed
Summary

RBPsuite is a new webserver that uses deep learning to predict RNA-binding protein (RBP) binding sites on both linear and circular RNAs, offering a faster and more accessible tool for researchers.

Keywords:
Circular RNAsDeep learningLinear RNAsRNA-binding proteins

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA-binding proteins (RBPs) are essential regulators of diverse biological processes.
  • Deep learning models show promise for predicting RBP binding sites on RNA.
  • Current deep learning methods for RBP site prediction are computationally demanding and time-consuming.

Purpose of the Study:

  • To develop an efficient and user-friendly webserver for predicting RBP binding sites on RNA.
  • To provide a tool that can handle both linear and circular RNA sequences.
  • To accelerate RBP binding site analysis in biological research.

Main Methods:

  • Development of RBPsuite, a deep learning-based webserver.
  • Utilizing updated iDeepS for linear RNA RBP binding site prediction.
  • Employing a newly developed CRIP tool for circular RNA (circRNA) RBP binding site prediction.
  • Segmenting RNA sequences into 101-nucleotide fragments for interaction scoring.
  • Identifying verified motifs within binding segments and analyzing binding score distribution.

Main Results:

  • RBPsuite accurately predicts RBP binding sites on linear and circular RNAs.
  • The webserver provides RBP binding scores for RNA segments.
  • Motif detection and binding score distribution analysis are integrated features.
  • The tool offers an accessible platform for RBP binding site prediction.

Conclusions:

  • RBPsuite is an easy-to-use online webserver for predicting RBP binding sites.
  • The tool is freely available for researchers at http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/.
  • RBPsuite facilitates the study of RNA-protein interactions in various RNA types.