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ucsc-conservation-and-tfbs

Fetch UCSC phyloP and phastCons conservation metrics with TFBS annotations for genomic coordinates.

2.7k|283|Updated May 13, 2026
Search Tags:#genomics#variant interpretation#tfbs#evolutionary conservation#u csc genome browser#phyloP#phastCons
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill ucsc-conservation-and-tfbs
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ucsc-conservation-and-tfbs
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/ucsc_conservation_and_tfbs
Command: npx skills add https://github.com/google-deepmind/science-skills --skill ucsc-conservation-and-tfbs

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

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.

Frequently Asked Questions about ucsc-conservation-and-tfbs

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve phyloP and phastCons conservation scores for a genomic variant?▼

To retrieve phyloP and phastCons conservation scores, you query UCSC comparative genomics tracks with your genomic coordinates. This Skill fetches site-level phyloP constraints and region-level phastCons conserved elements for hg38 or hg19 assemblies.

What is the best way to check if a non-coding SNV impacts transcription factor binding sites?▼

Checking transcription factor binding site (TFBS) impact involves querying UCSC TFBS tracks for your variant's interval. This Skill retrieves ENCODE clusters, JASPAR predictions, and ReMap ChIP-seq atlas evidence to identify disrupted regulatory proteins.

Can I use UCSC genome browser tracks to find evolutionary acceleration signals in regulatory regions?▼

Yes, you can use UCSC genome browser tracks to find evolutionary acceleration signals by computing summary statistics for phyloP scores. This Skill applies an optional acceleration heuristic to flag likely evolutionary acceleration in your specified intervals.

Does this conservation and TFBS retrieval approach support both hg19 and hg38 assemblies?▼

Yes, this conservation and TFBS retrieval approach supports both hg19 and hg38 assemblies. It applies appropriate track mappings for vertebrate, mammal, and primate comparative genomics collections to fetch phyloP, phastCons, and TFBS data.

How do I filter transcription factor binding site results for specific genomic coordinates?▼

You filter transcription factor binding site results by executing wrapper scripts for UCSC REST track queries with optional TF filtering. This allows configurable collections and robust coordinate parsing to output targeted TFBS evidence to a file.

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