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Genome relationships and functional differences

Comparative microbial genomics

Investigate how selected microbial genomes differ in evolutionary relationships, functional potential and genomic context. We focus comparisons on a defined biological question, from strain identity to a particular pathway or gene family.

Who this service is for

For isolate-genome and genome-resolved researchers comparing strains, lineages, habitats or traits. Projects include functional repertoire comparisons, candidate enzyme investigation and placing newly sequenced isolates alongside carefully chosen public references.

Discuss this analysis

From inputs to interpretation

Analysis workflow

The final workflow is agreed after reviewing your data. Optional modules are selected for suitability and the research question.

  1. Define a comparable genome set

    Review quality, taxonomic breadth, sampling and redundancy. Document inclusion criteria and exclusions so their effect on the comparison can be assessed.

  2. Harmonise annotation and relationships

    Use consistent annotation where needed and examine genomic similarity and phylogenetic relationships. Choose suitable orthologs or conserved markers for the organisms and scale of comparison.

  3. Compare functions and context

    Assess agreed gene families, pathways and functional categories. Inspect locus organisation or synteny when assemblies support it, distinguishing annotation differences from credible biological differences.

  4. Integrate biological evidence

    Relate genome patterns to source or phenotype metadata. Evaluate alternative explanations including relatedness, uneven sampling and incomplete genomes before proposing ecological or functional hypotheses.

Statistics and study design

Genome-distance summaries and scoped tests of functional representation may be included. Relatedness, genome size, sampling balance and multiple testing are considered where relevant. A small convenience sample should not be treated as representative of an entire habitat or species.

Biological interpretation

Annotation indicates functional potential, not experimental verification. Missing annotations may reflect assembly gaps, gene-calling differences or reference limitations. Candidate adaptation, horizontal transfer and pathway differences need supporting context and may remain hypotheses.

Outputs and deliverables

  • A genome inventory with provenance, inclusion decisions, taxonomy and quality summaries.
  • Similarity and phylogenetic outputs, plus scoped gene-family, pathway or locus comparisons.
  • Interpretation notes, publication-oriented figures and methods documenting the comparison strategy and database versions.

Scientific visualisations

ANI or genome-distance heatmaps, annotated trees, gene-family/pathway heatmaps and locus or synteny comparisons where data permit. Figures connect genome metadata and the comparison set to the biological question.

Scientific figure preparation

How does this differ from pangenome analysis?

Comparative genomics is the broader investigation of relationships, functions and genome context. Pangenome analysis specifically defines gene families shared or variable across a suitable collection. A targeted pathway or locus comparison may not need a full pangenome; a gene-repertoire question often does.

Scope your project

Tell us about your dataset.

Describe the genome set, quality information, comparison groups and pathways or traits of interest. Include public accession identifiers if references are already selected.

Send a brief description first. We agree data transfer, analysis scope, deliverables and a project-specific quotation before work begins.

Start a project enquiry

BiomeLens provides bioinformatics and data analysis services. Laboratory sequencing, DNA/RNA extraction and wet-lab sample processing are not part of our services.