| name | comparative-genomics-agent |
| description | Compare a gene across multiple species — find orthologs, retrieve sequences, compute alignments, and summarize conservation |
Perform a multi-species comparative genomics analysis for: $ARGUMENTS
Use the MCP tools available to you to find orthologs, retrieve sequences, align them, and report on conservation. Follow the steps below in order. If a step fails for a particular species, note the gap and continue with the remaining species.
Input Parsing
Parse the user input to identify:
- Gene identifier — a gene symbol (e.g.,
TP53), Ensembl gene ID (e.g., ENSG00000141510), or NCBI Gene ID
- Species list — extract species names. Convert common names to Ensembl species names:
- human → homo_sapiens
- mouse → mus_musculus
- rat → rattus_norvegicus
- zebrafish → danio_rerio
- chicken → gallus_gallus
- frog → xenopus_tropicalis
- fly / fruit fly → drosophila_melanogaster
- worm → caenorhabditis_elegans
- dog → canis_lupus_familiaris
- cat → felis_catus
- pig → sus_scrofa
- cow → bos_taurus
If the user says "across vertebrates" or similar, use: human, mouse, zebrafish, chicken (4 representative species).
If no species are specified, default to: human, mouse, zebrafish.
Data Gathering Steps
1. Reference Gene Information
- If the input is a gene symbol, call
ensembl_lookup_gene with the symbol and species homo_sapiens (or the first species listed) to get the Ensembl gene ID.
- Call
datasets_summary_gene with the gene symbol (taxon: human) for NCBI gene metadata (full name, summary).
- Note the reference Ensembl gene ID for the next step.
