skills.rest
nguyenhungtran18
nguyenhungtran18COMMUNITY
Explore all skills by this author →
GitHub

ucsc-conservation-and-tfbs

Fetch evolutionary conservation scores and transcription factor binding sites from the UCSC Genome Browser API.

1|Updated Aug 31, 2026
Search Tags:#genomics#variant analysis#tfbs#phyloP#phastCons#ucsc genome browser#conservation scores
One-click install
npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill ucsc-conservation-and-tfbs-nguyenhungtran18
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ucsc-conservation-and-tfbs
Source: https://github.com/nguyenhungtran18/skill-and-tool-tracker/tree/main/skills/ucsc_conservation_and_tfbs
Command: npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill ucsc-conservation-and-tfbs-nguyenhungtran18

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) components.

What problem does it solve? Interpreting non-coding genomic variants requires knowing whether a site is evolutionarily conserved or overlaps a transcription factor binding site, but querying the UCSC Genome Browser API manually involves track-name discovery, coordinate conversion, and rate-limit handling. ## Core Features & Use Cases - Conservation Scores: Retrieve phyloP and phastCons scores for variants or regions across vertebrate, mammal, and primate alignments on hg38 or hg19. - TFBS Lookup: Query ENCODE, JASPAR, and ReMap transcription factor binding site tracks with optional TF-name filtering. - Track Discovery & Acceleration Analysis: List available UCSC tracks by search term or group, and compute heuristic evolutionary-acceleration statistics for a locus. - Use Case: Given a non-coding SNV at chr1:215867804, fetch its phyloP100way score to assess pathogenicity, then check whether it disrupts a TP53 binding site from the JASPAR track. ## Quick Start Ask the AI to check whether the variant at chr1:215867804 is evolutionarily conserved and whether it overlaps any transcription factor binding sites on hg38.

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 get phyloP and phastCons conservation scores for a genomic variant?▼

Run scripts/get_conservation.py with --coordinates like "chr1:215867804" and --output for the JSON result file. phyloP is the best metric for individual bases, while phastCons suits functional windows due to HMM smoothing.

How to find transcription factor binding sites for a genomic region?▼

Run scripts/get_tfbs.py with --coordinates and --tracks such as encRegTfbsClustered, jaspar2024, or ReMapTFs. Use --tf-filter with a substring like TP53 to keep only matching TFName entries from large JASPAR result sets.

Which genome assemblies and alignments does UCSC conservation querying support?▼

Both hg38 and hg19 are supported, with hg38 as the default. Collections include the 100-vertebrate Multiz alignment, the Hiller Lab 470-way mammalian alignment (hg38), 30-primate alignment, and legacy 46-way subsets for hg19.

Why does querying the jaspar or ReMap track return a 400 error?▼

Tracks named jaspar or ReMap without a year are container tracks and fail with a 400 error. Always use a specific subtrack name such as jaspar2026 or ReMapTFs, which you can discover with scripts/list_tracks.py.

What are the limitations of conservation scores for variant interpretation?▼

Conservation scores measure how much sites have changed, not the ancestral nucleotide state. Low conservation does not strictly mean neutral sequence, since it can also reflect a high local mutation rate that scores alone cannot distinguish.

Related Skills

Explore More Education & Research Skills→
SciMate-AISciMate-AI
1

pysam

Read and analyze BAM, VCF, and FASTA genomic data in Python.

Official
Advanced
nahisahonahisaho
3

scientific-variant-effect-prediction

Integrate AlphaMissense, CADD, and SpliceAI to score and classify variant pathogenicity.

Community
Advanced
ammawlaammawla
26

gnomad-variants

Query gnomAD allele frequencies and gene constraint scores via GraphQL API.

Community
Intermediate
arslan9024arslan9024

ucsc-conservation-and-tfbs

Fetch evolutionary conservation scores and transcription factor binding sites from the UCSC Genome Browser API.

Community
Intermediate