Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

Bioinformatics. 2016 Aug 15;32(16):2419-26. doi: 10.1093/bioinformatics/btw209. Epub 2016 Apr 19.


Motivation: Computational prediction of transcription factor (TF) binding sites in the genome remains a challenging task. Here, we present Romulus, a novel computational method for identifying individual TF binding sites from genome sequence information and cell-type-specific experimental data, such as DNase-seq. It combines the strengths of previous approaches, and improves robustness by reducing the number of free parameters in the model by an order of magnitude.

Results: We show that Romulus significantly outperforms existing methods across three sources of DNase-seq data, by assessing the performance of these tools against ChIP-seq profiles. The difference was particularly significant when applied to binding site prediction for low-information-content motifs. Our method is capable of inferring multiple binding modes for a single TF, which differ in their DNase I cut profile. Finally, using the model learned by Romulus and ChIP-seq data, we introduce Binding in Closed Chromatin (BCC) as a quantitative measure of TF pioneer factor activity. Uniquely, our measure quantifies a defining feature of pioneer factors, namely their ability to bind closed chromatin.

Availability and implementation: Romulus is freely available as an R package at


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Binding Sites*
  • Chromatin
  • Chromatin Immunoprecipitation
  • Computational Biology / methods*
  • Protein Binding*
  • Sequence Analysis, DNA
  • Transcription Factors*


  • Chromatin
  • Transcription Factors