ucsc-conservation-and-tfbs

What problem does it solve?

This Skill helps you determine whether genomic variants or regulatory regions show evidence of evolutionary constraint and potential transcription factor binding impact.

Core Features & Use Cases

• Evolutionary constraint retrieval: Fetches UCSC phyloP (site-level constraint) and phastCons (region-level conserved elements) from comparative genomics multiple alignments.
• TF binding site lookup: Queries UCSC TFBS tracks (e.g., ENCODE clusters, JASPAR predictions, ReMap ChIP-seq atlas) for intervals to interpret non-coding variant mechanisms.
• Lineage-specific control: Supports vertebrate/mammal/primate collections and both hg38 and hg19 assemblies (with appropriate track mappings).
• Optional acceleration heuristic: Can compute summary statistics for phyloP scores and flag likely evolutionary acceleration signals.
• Use Case: If you have an SNV or an enhancer interval, use phyloP/phastCons to assess conservation and use TFBS tracks to identify which regulatory proteins’ binding might be disrupted.

Quick Start

Use the ucsc_conservation_and_tfbs skill to fetch phyloP/phastCons conservation scores and optional TFBS for a specified hg38 coordinate range for your variant or regulatory element.