Does this skill support legacy assemblies like GRCh37?

Yes, it provides specific guidance and endpoints for querying GRCh37/hg19 as well as mapping coordinates between older and current genome assemblies.

How does it handle API rate limiting?

The skill includes logic and best practices for handling 429 status codes, respecting 'Retry-After' headers, and limiting requests to the maximum 15 per second allowed by Ensembl.

Can I perform batch queries for multiple genes?

Yes, the skill is designed to follow Ensembl REST API best practices, including the use of batch endpoints to efficiently query multiple items while respecting rate limits.

What kind of sequences can I retrieve?

You can retrieve genomic DNA, transcript (cDNA), and protein sequences in various formats including JSON and FASTA.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: Activer007

byActiver007

0•

데이터 과학 및 ML

Queries and analyzes genomic data from the Ensembl REST API for gene lookups, sequence retrieval, and variant analysis.

This skill empowers genomic researchers and bioinformaticians to interact directly with the Ensembl database, a premier resource for vertebrate genomic information. It provides seamless access to the Ensembl REST API, enabling users to perform gene symbol lookups, retrieve DNA and protein sequences, and execute complex variant effect predictions (VEP). Beyond simple queries, the skill supports comparative genomics for identifying orthologs across 250+ species and includes tools for genomic coordinate mapping between assemblies like GRCh37 and GRCh38, making it an essential utility for automating bioinformatics pipelines and data analysis workflows.

주요 기능

01Coordinate mapping between various genome assembly versions

02Variant analysis and functional consequence prediction via VEP

03Gene and transcript information retrieval by symbol or Ensembl ID

04High-throughput sequence fetching for DNA, cDNA, and proteins

05Comparative genomics tools for ortholog and paralog identification

060 GitHub stars

사용 사례

01Predicting the functional impact of genetic variants in clinical research

02Automating gene annotation and sequence extraction for bioinformatics pipelines

03Conducting cross-species evolutionary analysis and ortholog mapping

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills ensembl-database

For use in Claude.ai and ChatGPT

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