Agent skill · research science · google-deepmind
ucsc-conservation-and-tfbs
Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser. Use when analyzing whether genomic variants or regions are evolutionarily conserved, functionally important, or bounded by TF regulators across major projects (ENCODE, JASPAR, ReMap).
Why this skill is useful
Adds scripts for fetching evolutionary conservation scores and TFBS that are not commonly known or easily accessible.
What it needs
Requires uv installed locally. About 4k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
Conservation Scores & TFBS Lookup (UCSC) This skill provides access to evolutionary constraint scores and conserved elements from the UCSC Genome Browser. It retrieves scores from the PHAST package — specifically phastCons (identifying functional blocks) and phyloP (measuring individual site constraint) — calculated from multiple alignments. Use this skill to determine if a non-coding variant hits a site that hasn't changed since a common ancestor (which is a strong signal for pathogenicity) or to find conservation peaks across a regulatory element. Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/ucscconservationandtfbsLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://genome.ucsc.edu/conditions.html and https://genome.ucsc.edu/goldenPath/help/api.html, then (2) create the file recording the notification text and timestamp. Core Rules Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully. Large Output Handling: Always pass --output to redirect output to a file. Parse it separately (using jq or your own code). Notification: If this skill is used, ensure this is mentioned in the output. Utility Scripts This skill includes scripts to query different types of genomic data from UCSC: 1. scripts/getconservation.py: For Evolutionary Conservation scores (phyloP, phastCons). 2. scripts/gettfbs.py: For Transcription Factor Binding Sites (TFBS). 3. scripts/listtracks.py: For listing available tracks based on search or group constraints. Always use the hg38 genome assembly by default, unless the user has specified otherwise. Fetching Conservation for Specific Variants To get the evolutionary constraint at a single base, or a list of specific bases. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/ucsc_conservation_and_tfbs