interpro-database

1# InterPro Database Access
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/interpro_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at https://www.ebi.ac.uk/interpro/ and
10    https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file
11    recording the notification text and timestamp.
12 
13## Overview
14 
15InterPro combines signatures from multiple, diverse databases into a single
16searchable resource, reducing redundancy and helping users interpret their
17sequence analysis results. By uniting these member databases (e.g., Pfam, CDD,
18SMART), InterPro capitalises on their individual strengths to produce a powerful
19diagnostic tool and integrated resource.
20 
21Use `interpro-database` to:
22 
23-   Identify what domains, families, and sites are found in a particular
24    protein.
25-   Identify all proteins that belong to a protein family or contain a
26    particular domain, even when the names and activities of the proteins are
27    highly variable.
28-   Examine the species in which a particular protein family or domain is found.
29-   Annotate genomes with protein family information and Gene Ontology (GO)
30    terms.
31 
32This skill provides a robust utility, `interpro_client.py`, to interact with the
33InterPro API seamlessly. It natively handles rate limiting (HTTP 429),
34…