What species are supported by the Ensembl Database skill?

The skill supports over 250 vertebrate species, including humans (Homo sapiens), mice (Mus musculus), zebrafish (Danio rerio), and fruit flies (Drosophila melanogaster).

How does the skill handle Ensembl API rate limits?

The skill is designed to respect the Ensembl REST API limit of 15 requests per second and includes logic to handle 429 'Too Many Requests' responses by checking the Retry-After header.

Can I use this skill to convert genomic coordinates?

Yes, the skill provides assembly mapping capabilities to convert coordinates between different genome versions, such as mapping from GRCh37 (hg19) to GRCh38.

Does this skill support the Variant Effect Predictor (VEP)?

Yes, the skill includes core capabilities for querying VEP to predict the functional consequences of genetic variants using HGVS notation or rsIDs.

Do I need any specific Python packages to use this skill?

While it can work with standard libraries like 'requests', it is recommended to have 'ensembl_rest' installed for a more robust and Pythonic interface to the API endpoints.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: Activer007

byActiver007

데이터 과학 및 ML

Queries the Ensembl REST API to retrieve genomic annotations, sequences, and variant data for over 250 vertebrate species.

소개

The Ensembl Database skill provides a specialized interface for programmatically interacting with the EMBL-EBI Ensembl genome database, a premier resource for vertebrate genomic data. It enables researchers and developers to perform complex biological queries including gene symbol lookups, multi-format sequence retrieval, and functional variant analysis via the Variant Effect Predictor (VEP). By streamlining access to comparative genomics, ortholog mapping, and assembly coordinate conversions (such as GRCh37 to GRCh38), this skill significantly accelerates the development of bioinformatics pipelines and genomic research workflows within the Claude environment.

주요 기능

Multi-format sequence retrieval for DNA, cDNA, and proteins
Comparative genomics for identifying orthologs and paralogs
Gene and transcript annotation lookup by symbol or Ensembl ID
Genomic coordinate conversion between GRCh37 and GRCh38 assemblies
Variant Effect Predictor (VEP) for functional consequence mapping
0 GitHub stars

사용 사례

Analyzing genetic variants and predicting their functional impact on protein coding
Building automated bioinformatics pipelines for gene annotation and data extraction
Mapping evolutionary relationships and conservation across multiple vertebrate species

소개

주요 기능

Multi-format sequence retrieval for DNA, cDNA, and proteins
Comparative genomics for identifying orthologs and paralogs
Gene and transcript annotation lookup by symbol or Ensembl ID
Genomic coordinate conversion between GRCh37 and GRCh38 assemblies
Variant Effect Predictor (VEP) for functional consequence mapping
0 GitHub stars

사용 사례

Analyzing genetic variants and predicting their functional impact on protein coding
Building automated bioinformatics pipelines for gene annotation and data extraction
Mapping evolutionary relationships and conservation across multiple vertebrate species