PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays

Bo Li, Akshay Tambe, Sharon Aviran, Lior Pachter

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. We introduce PROBer, a statistical model and associated software, that addresses this challenge for the analysis of toeprinting assays. PROBer takes sequencing data as input and outputs estimated transcript abundances and isoform-specific modification profiles. Results on both simulated and biological data demonstrate that PROBer significantly outperforms individual methods tailored for specific toeprinting assays. Since the space of toeprinting assays is ever expanding and these assays are likely to be performed and analyzed together, we believe PROBer's unified data analysis solution will be valuable to the RNA community.

Original languageEnglish (US)
Pages (from-to)568-574.e7
JournalCell Systems
Issue number5
StatePublished - May 24 2017


  • bioinformatics
  • post-transcriptional modification of RNA nucleotides
  • post-transcriptional regulation
  • RNA structure probing
  • RNA-protein interactions
  • toeprinting by high-throughput sequencing

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology


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