- Description
- PIQ is a computational method that models the magnitude and shape of genome-wide DNase profiles to facilitate the identification of transcription factor (TF) binding sites. The input of PIQ is one or more DNase-seq experiments, the genome sequence of the organism assayed and a list of motifs represented as position weight matrices (PWMs) that describe candidate TF binding sites. PIQ uses machine learning methods to normalize input DNase-seq data and then predicts TF binding by detecting both the shape and magnitude of DNase profiles specific to each TF. The output of PIQ is the probability of occupancy for each candidate binding site in the genome, along with aggregate TF-specific scores (e.g. metrics for TF-specific chromatin opening).
- Software type
- database
- Used for
- community resource