uniprot-database

To retrieve FASTA protein sequences, query the UniProt REST API endpoints directly using HTTP requests. The Skill provides Python helper scripts to automate this process, supporting both single entry retrieval by accession and batch processing for large datasets.

You can map UniProt identifiers to Ensembl, RefSeq, PDB, and GO terms using the UniProt REST API ID mapping functionality. The Skill includes helper functions and references to supported mapping databases to enable cross-database identifier translation.

UniProt batch search by organism and GO terms is performed by constructing specific query syntax against the UniProt REST API. The Skill supports field customization and streaming of large result sets to handle extensive protein datasets efficiently.

The UniProt REST API supports streaming large result sets for batch retrieval workflows. This Skill enables streaming to handle big datasets when searching protein entries or retrieving sequences, preventing memory bottlenecks during automated processing.

Swiss-Prot contains reviewed protein annotations curated by experts, while TrEMBL holds unreviewed computationally generated entries. The Skill provides direct REST access to both datasets, allowing you to filter queries and retrieve entries based on annotation quality.

You need the Python requests library to use this Skill, as it handles direct HTTP/REST queries against UniProt endpoints. The Skill includes Python client scripts with helper functions built on requests to search entries, map IDs, and retrieve sequences.