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  1. Home
  3. Smtrackr: An R/bioconductor Package For Mapping Protein Binding At Individual Dna Molecules.
  1. Home
  3. Smtrackr: An R/bioconductor Package For Mapping Protein Binding At Individual Dna Molecules.

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SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules.

Aashna Bansal1, Himani Barmola1, Shivam Yadav1

  • 1Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India.

Bioinformatics Advances
|June 25, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

SMTrackR visualizes protein-DNA binding states from single-molecule sequencing data, offering a user-friendly tool for analyzing transcription factor and histone complex interactions. This R/Bioconductor package enables quantification and visualization of DNA binding states, advancing epigenomic research.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Epigenetics

Background:

  • Single-molecule sequencing assays (NOMe-seq, dSMF, Nanopore) offer advantages over traditional methods like DNase-seq and ATAC-seq by preserving DNA integrity.
  • These advanced techniques allow for the simultaneous quantification of protein-free DNA, transcription factor-bound DNA, and histone complex-bound DNA states.
  • A need exists for a user-friendly computational tool to visualize and quantify these distinct protein-DNA binding states at the single-molecule level.

Purpose of the Study:

  • To introduce SMTrackR, a novel R/Bioconductor package designed for the visualization and quantification of protein-DNA binding states on individual DNA molecules.
  • To provide researchers with a tool that leverages single-molecule sequencing data to understand gene regulation and chromatin accessibility.

Main Methods:

  • SMTrackR queries a pre-built single-molecule footprint database hosted on a Galaxy Server, utilizing BigBed files derived from NOMe-seq, dSMF, and Nanopore (SMAC-seq) datasets.
  • The package employs the UCSC REST API to access BigBed files, enabling the plotting of footprint heatmaps categorized by binding states and reporting their occupancies.
  • SMTrackR generates Gviz-compatible scripts for visualizing individual DNA molecules alongside gene tracks, facilitating integrated analysis.

Main Results:

  • SMTrackR successfully visualizes and quantifies protein-DNA binding states from various single-molecule sequencing data types.
  • The tool provides detailed footprint heatmaps and occupancy statistics, offering insights into chromatin accessibility and transcription factor binding.
  • Generated Gviz scripts allow for the visualization of single-molecule data in the context of genomic features.

Conclusions:

  • SMTrackR addresses the lack of user-friendly tools for analyzing single-molecule sequencing data related to protein-DNA interactions.
  • The package enhances the utility of NOMe-seq, dSMF, and Nanopore sequencing by providing robust visualization and quantification capabilities.
  • SMTrackR is implemented in R, available as a Bioconductor package, and includes a web version and pipelines for data generation, promoting accessibility and broad adoption in epigenomic research.