Comparative Genomics & Ortholog Analysis

Comparative Genomics & Ortholog Analysis

Cross-species gene comparison, ortholog identification, sequence retrieval, and functional conservation analysis integrating Ensembl Compara, NCBI, UniProt, OLS, Monarch, and OpenTargets.

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first (PubMed, UniProt, ChEMBL, ClinVar, etc.) rather than reasoning from memory. A database-verified answer is always more reliable than a guess.

COMPUTE, DON'T DESCRIBE

When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.

When to Use This Skill

Triggers:

• "Find the mouse ortholog of [human gene]"
• "Compare [gene] across species"
• "Is [gene] conserved in [organism]?"
• "What are the orthologs of [gene]?"
• "Cross-species comparison of [gene/protein]"
• "Evolutionary conservation of [gene]"
• "Compare GO annotations between human and mouse [gene]"

Use Cases:

1. Ortholog Discovery: Find equivalent genes in other species for a human gene
2. Conservation Analysis: Assess how conserved a gene is across evolutionary distance
3. Functional Comparison: Compare GO terms, domains, and annotations across orthologs
4. Model Organism Selection: Determine which model organism best recapitulates human gene function
5. Gene Tree Analysis: Visualize evolutionary history of a gene family
6. Cross-Species Phenotype Bridging: Link human disease phenotypes to model organism phenotypes via orthologs

Conservation Reasoning Framework

Understanding conservation requires distinguishing between types of evolutionary patterns and what they imply about function.

High conservation signals functional constraint. When a gene is maintained as a 1:1 ortholog from yeast to humans, purifying selection has prevented sequence divergence — the gene's function is essential and cannot be easily altered. Highly conserved positions within a protein sequence (high PhastCons scores > 0.8, or GERP RS > 4) are under strong constraint; mutations at these positions are disproportionately pathogenic. For non-coding regions, conservation in mammals at PhastCons > 0.5 suggests a candidate regulatory element.

Low conservation in one lineage has two possible explanations: relaxed selection or positive selection. Use the dN/dS ratio (nonsynonymous to synonymous substitution rate) to distinguish them. A dN/dS ratio near 1 suggests neutral evolution — the gene is no longer under purifying selection (relaxed constraint, possibly reflecting loss of function in that lineage). A dN/dS ratio > 1 indicates positive selection — the gene is diverging faster than neutral expectation, often because it is adapting to a new environment or function. A dN/dS ratio << 1 is the signature of purifying selection (functional constraint). When a vertebrate gene shows high divergence in a specific branch of the tree, ask which explanation applies before concluding that function is lost.

Computing dN/dS. The data path: ensembl_get_homology(...) → the 1:1 ortholog IDs → EnsemblSeq_get_id_sequence(id=..., type="cds") for each → codon-align the two CDS (orthologous CDS are usually directly alignable; for divergent pairs align the protein and back-translate) → compute dN/dS. Prefer the Sequence_dn_ds tool — one call returns structured dN, dS, dN_dS, per-site counts, and an interpretation: