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Conservation Scores & TFBS Lookup (UCSC) · mkurman | DecimalAI

scienceby mkurman

Conservation Scores & TFBS Lookup (UCSC)

mkurman/ucsc-conservation-and-tfbs

Source mkurman/zorai ↗License MIT

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.

NewMaintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

3 of 22 test cases passed with the skill.

Pass-rate lift: —
Tokens: +41%
Agent turns: 0%
Response time: -26%

Model gemini-3.6-flashMeasured 8/21/2026v13 of 22 cases passed with skill · 5 comparable

Tokens, turns and time describe resource use, not a dollar price.

Lift withheld: 5 comparable cases; this report requires 8.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-ucsc-conservation-and-tfbs/SKILL.md https://app.decimal.ai/s/mkurman-ucsc-conservation-and-tfbs/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-ucsc-conservation-and-tfbs, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-ucsc-conservation-and-tfbs/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-ucsc-conservation-and-tfbs

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-ucsc-conservation-and-tfbs/SKILL.md https://app.decimal.ai/s/mkurman-ucsc-conservation-and-tfbs/SKILL.md

Raw file: /s/mkurman-ucsc-conservation-and-tfbs/SKILL.md ↗ · machine-readable summary at /s/mkurman-ucsc-conservation-and-tfbs.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

A test case the skill fixed. Same model, same prompt, with and without the skill.

Prompt

A paper reports non-coding constraint on GRCh37 at chr5:1045330-1046172 using the older 46-vertebrate Multiz alignment. I want to save results to /tmp/vert46_cons.json. How should the query be configured to hit the 46-way vertebrate alignment instead of the 100-way default?

What was checked, without and with the skill
Checked	Without skill	With skill
Passes --collection vertebrate46 when querying hg19 legacy vertebrate alignments	Missed	Passed
Selects hg19 genome assembly instead of the default hg38 build	Passed	Passed

case-05 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md173 lines4 filesincludes scripts

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

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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:

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

Track record

Benchmark

3 / 22

test cases passed with the skill

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/ucsc_conservation_and_tfbs/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 3 files · scripts

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

Conservation Scores & TFBS Lookup (UCSC)

Prerequisites

Core Rules

Utility Scripts

Track record

Benchmark

Adoption

SkillSafety

Source

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