# Ucsc Conservation And Tfbs

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill ucsc-conservation-and-tfbs -g -a gemini-cli -y`

## Description

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).

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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/ucsc_conservation_and_tfbs_LICENSE.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/get_conservation.py`**: For Evolutionary Conservation scores
    (phyloP, phastCons).
2.  **`scripts/get_tfbs.py`**: For Transcription Factor Binding Sites (TFBS).
3.  **`scripts/list_tracks.py`**: For listing available tracks based on search
    or group constraints.

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/ucsc_conservation_and_tfbs/SKILL.md