The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill ingests data from external sources (ColabFold and EBI APIs) and user-provided FASTA files to generate protein similarity reports.
Ingestion points: Biological sequence data and metadata returned from the MMseqs2 and BLAST APIs are parsed and written to Markdown and JSON files.
Boundary markers: No explicit delimiters are used in the generated Markdown to separate untrusted API content from agent instructions.
Capability inventory: The skill uses uv run for script execution, performs network requests to external APIs, and writes result files to the local workspace.
Sanitization: While the scripts parse specific numeric and identifier fields, there is no comprehensive sanitization of the protein descriptions or metadata strings returned by the remote services.
[EXTERNAL_DOWNLOADS]: The skill communicates with scientific web services to perform protein searches.
Fetches search results and archives from api.colabfold.com and www.ebi.ac.uk.
These are well-known bioinformatics resources used for legitimate research purposes.
[COMMAND_EXECUTION]: The skill provides instructions for the agent to execute local Python scripts using the uv tool.
Commands are used to run scripts/mmseqs2_search.py and scripts/uniprot_blast.py with user-defined parameters.
[DATA_EXPOSURE_AND_EXFILTRATION]: The skill accesses the ~/.env file to retrieve the USER_EMAIL environment variable.
This information is used for job tracking in headers sent to the EBI BLAST API, following the skill's defined protocol for handling user credentials.

protein-sequence-similarity-search