ucsc-browser

What problem does it solve?

This Skill enables users to programmatically access UCSC Genome Browser's extensive genomic annotations, sequences, and track data to support genome research and analysis workflows.

Core Features & Use Cases

• Track Discovery: List available tracks for a specified genome assembly and identify ENCODE-specific regulation tracks.
• Region Data Retrieval: Obtain cCRE annotations, TF binding clusters, conservation scores, and other regulatory features within user-defined genomic regions.
• Sequence Extraction: Fetch DNA sequences and reverse complements for motif discovery, variant analysis, or CRISPR design.
• Data Integration: Combine UCSC track data with ENCODE experiment information for comprehensive regulatory analysis and visualization.

Quick Start

Query the UCSC API to retrieve cCRE annotations overlapping a given genomic locus and fetch the corresponding DNA sequence for downstream motif analysis.