Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.
User Notification: If
.licenses/protein_sequence_similarity_search_LICENSE.txt does not already
exist in the workspace root directory then (1) prominently notify the user
to check the terms at https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast and
https://colabfold.com, then (2) create the file recording the notification
text and timestamp.
.env file: Make sure the .env file exists in your home directory.
Create one if it does not exist.
USER_EMAIL (optional but recommended): Recommended by the EBI for
BLAST job tracking, but the skill works without it. You MUST use the
safe credentials protocol in the credentials skill to check for and
request this credential if this skill looks relevant to the user's request.
