protein-sequence-similarity-search

1## Prerequisites
2 
31.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
4    `uv` is installed and on PATH.
52.  **User Notification**: If
6    .licenses/protein_sequence_similarity_search_LICENSE.txt does not already
7    exist in the workspace root directory then (1) prominently notify the user
8    to check the terms at https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast and
9    https://colabfold.com, then (2) create the file recording the notification
10    text and timestamp.
113.  **`.env` file**: Make sure the `.env` file exists in your home directory.
12    Create one if it does not exist.
134.  **`USER_EMAIL`** (optional but recommended): Recommended by the EBI for
14    BLAST job tracking, but the skill works without it. You **MUST** use the
15    safe credentials protocol in the `credentials` skill to check for and
16    request this credential if this skill looks relevant to the user's request.
17 
18## Goal
19 
20Take a user-provided amino acid sequence (or a path to a `.fasta` file), search
21for sequence homologues using the fastest available method, generate a
22Markdown-formatted table of the top hits, interpret key alignment metrics,
23summarize the inferred protein functions, and save results locally for future
24programmatic analysis.
25 
26## Core Rules
27 
28-   **Strict Validation**: For BLAST, only use database codes listed in the
29    table below.
30-   **No Hallucinations**: If a script throws an error or returns no hits,
31…