UROPA

UROPA annotates genomic ranges to assign biological context to peaks from high-throughput sequencing experiments, including transcription factor binding sites (TFBS), histone modification ChIP-seq, and chromatin accessibility assays such as ATAC-seq.

Key Features:

• Universal annotation capability: Annotates diverse genomic ranges (peaks) from high-throughput sequencing experiments and assigns biological context.
• Configurable prioritization: Supports prioritization of target features via multiple integrated queries with parameters including feature type, distance from the peak, strand specificity, feature attributes (e.g., protein-coding genes), and anchor position relative to the genomic feature.
• Integration with multiple reference annotations: Accepts reference annotation files in GTF format from GENCODE, Ensembl, RefSeq, and custom GTF files.
• Comprehensive statistical summaries and visualization: Produces statistical summaries and plots that describe the annotation results.

Scientific Applications:

• Transcription factor binding site annotation: Annotation of TFBS peaks from ChIP-seq experiments.
• Histone modification annotation: Annotation of histone modification peaks from ChIP-seq experiments.
• Chromatin accessibility annotation: Annotation of chromatin accessibility peaks from ATAC-seq and related assays.
• General genomic-range interpretation: Interpretation of other genomic predictions and analyses that produce coordinate ranges.

Methodology:

Operates via a configuration file-based approach to define and prioritize target features and query parameters; implemented in Python and R for data processing and statistical analysis.