skills.rest
sanand0
sanand0COMMUNITY
Explore all skills by this author →
WebsiteGitHub

ensembl-database

Access Ensembl REST API for gene lookups, sequence retrieval, and VEP variant analysis.

8|Updated Nov 19, 2025
Search Tags:#bioinformatics#genomics#comparative genomics#variant analysis#ensembl#gene lookup
One-click install
npx skills add https://github.com/sanand0/scientific-research --skill ensembl-database-sanand0
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/ensembl-database
Command: npx skills add https://github.com/sanand0/scientific-research --skill ensembl-database-sanand0

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, ensembl_rest, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the Ensembl genome database, enabling researchers to query vast amounts of genomic data for over 250 species without needing to manually navigate complex web interfaces or download large datasets.

Core Features & Use Cases

  • Gene & Sequence Retrieval: Look up genes by symbol or ID, and retrieve their DNA, transcript, or protein sequences.
  • Variant Analysis: Predict the functional consequences of genetic variants using the Variant Effect Predictor (VEP).
  • Comparative Genomics: Find orthologs and paralogs across different species to understand evolutionary relationships.
  • Use Case: A researcher needs to find all known human genes that are orthologous to a specific mouse gene and retrieve their corresponding protein sequences for further analysis.

Quick Start

Use the ensembl-database skill to find orthologs for the human gene BRCA2 in the mouse species.

Frequently Asked Questions about ensembl-database

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

FAQPage Schema
How do I retrieve gene sequences from the Ensembl database using a REST API?▼

Retrieve Ensembl gene sequences by looking up genes via symbol or ID and extracting DNA, transcript, or protein sequences directly through the Ensembl REST API. This programmatic access fetches curated genomic annotations without manual web navigation.

What is the best way to find orthologs across different species for comparative genomics?▼

Find orthologs for comparative genomics by querying the Ensembl REST API across 250+ species. Identify orthologs and paralogs to understand evolutionary relationships and retrieve corresponding sequences for downstream analysis.

How do I predict functional consequences for genetic variants using VEP?▼

Predict functional consequences of genetic variants using the Variant Effect Predictor (VEP) accessed via the Ensembl REST API. Submit variants to VEP to analyze their impact on genes, transcripts, and protein sequences.

Can I use the Ensembl REST API for genomic research across multiple species?▼

Use the Ensembl REST API for genomic research across 250+ species. Query curated genomic annotations, perform gene lookups, and integrate retrieved data into existing genomic research pipelines programmatically.

How do I integrate Ensembl variant analysis and gene lookups into a bioinformatics pipeline?▼

Integrate Ensembl variant analysis and gene lookups into bioinformatics pipelines by sending programmatic requests to the Ensembl REST API. Automate sequence retrieval and VEP processing to output curated genomic data.

Related Skills

Explore More Education & Research Skills→
jimmc414jimmc414
557

ensembl-database

Retrieve genomic data from the Ensembl REST API for over 250 species.

Community
Intermediate
hxk622hxk622
8

ensembl-database

Queries the Ensembl genome database REST API for genes, variants, and orthologs.

Community
Intermediate
yf8578yf8578
1

sequence-analysis

Analyze DNA, RNA, and protein sequences with BioPython and command-line tools.

Community
Intermediate
jaechang-hitsjaechang-hits
298

ucsc-genome-browser

Retrieve genomic sequences and annotations from the UCSC Genome Browser REST API.

Community
Intermediate