nearBynding

The 'nearBynding' software tool is to investigate the preferences of RNA-binding proteins (RBPs) for RNA structures, contributing to the understanding of diseases driven by dysregulated mRNA metabolism. Implemented as an R/Bioconductor pipeline, 'nearBynding' incorporates information about RBP binding sites and RNA structure to discern the structural binding preferences of an RBP. The tool facilitates the visualization of RNA structure at and proximal to RBP binding sites transcriptome-wide, allows the analysis of CLIP-seq data without the need for peak-calling, and provides a flexible framework for studying RBP binding preferences about various RNA structure data types.

Topic

RNA immunoprecipitation;Gene transcripts;Nucleic acid structure analysis;Transcriptomics;Protein binding sites

Detail

  • Operation: Structure visualisation;RNA structure prediction;RNA binding site prediction;Expression analysis;Scaffolding

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: Johns Hopkins Bloomberg School of Public Health Start-up fund, the Predoctoral Fellowship in Informatics from the Pharmaceutical Research and Manufacturers of America Foundation, NIH.

  • Input: -

  • Output: -

  • Contact: Veronica Busa vbusa1@jhmi.edu

  • Collection: -

  • Maturity: Stable

Publications

  • nearBynding: A flexible pipeline characterizing protein binding to local RNA structure
  • Busa, V. F.; Favorov, A. V.; Fertig, E. J.; Leung, A. nearBynding: A flexible pipeline characterizing protein binding to local RNA structure. bioRxiv 2020. doi: 10.1101/2020.10.24.352591
  • https://doi.org/10.1101/2020.10.24.352591
  • PMID: -
  • PMC: -

Download and documentation

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