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

ABSTRACT:

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

SUBMITTER: Jankowski A 

PROVIDER: S-EPMC4978937 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature