What is the difference between Swiss-Prot and TrEMBL in this skill?

Swiss-Prot entries are manually curated and reviewed for high quality, while TrEMBL entries are computationally analyzed. You can filter for reviewed entries using the 'reviewed:true' query parameter.

Can this skill search for specific human genes?

Yes, you can use structured queries like 'gene:BRCA1 AND organism_id:9606' to find specific human proteins and their associated data.

Does it support mapping identifiers from other databases?

Yes, it includes robust ID mapping capabilities for dozens of databases including Ensembl, RefSeq, PDB, and AlphaFoldDB.

Can I download protein sequences in bulk?

Yes, the skill supports both batch retrieval of specific accessions and a streaming endpoint for downloading large datasets that exceed standard pagination limits.

UniProt Database Search & Mapping

Name: UniProt Database Search & Mapping
Author: lifangda

bylifangda

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Data Science & ML

Accesses the UniProt knowledgebase to search, retrieve, and map protein sequence and functional information.

About

This skill provides a specialized interface for the UniProt REST API, allowing Claude to perform complex protein database operations directly. It supports searching by gene, organism, or accession, retrieving sequences in FASTA format, and performing large-scale ID mapping across databases like Ensembl, RefSeq, and PDB. It is essential for bioinformatics workflows, protein analysis, and scientific data collection where precise, manually curated (Swiss-Prot) or computationally predicted (TrEMBL) protein data is required.

Key Features

16 GitHub stars
Batch retrieval and streaming for large-scale protein datasets
Granular field selection to optimize data transfer and processing
Cross-database ID mapping for Ensembl, RefSeq, PDB, and more
FASTA sequence retrieval and protein functional annotation access
Advanced search syntax for gene names, organisms, and protein accessions

Use Cases

Filtering and searching for reviewed Swiss-Prot entries with specific functional domains
Automating protein sequence retrieval for bioinformatics pipelines
Mapping large lists of identifiers between UniProt and other scientific databases

About

Key Features

16 GitHub stars
Batch retrieval and streaming for large-scale protein datasets
Granular field selection to optimize data transfer and processing
Cross-database ID mapping for Ensembl, RefSeq, PDB, and more
FASTA sequence retrieval and protein functional annotation access
Advanced search syntax for gene names, organisms, and protein accessions

Use Cases

Filtering and searching for reviewed Swiss-Prot entries with specific functional domains
Automating protein sequence retrieval for bioinformatics pipelines
Mapping large lists of identifiers between UniProt and other scientific databases