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Comparative Genome Viewer - Introduction


  • Overview of CGV
  • Demonstration of features
  • Explore on your own


Why use CGV?

At a high level, it is good for generating hypotheses, that is, finding interesting patterns and differences that can be investigated further experimentally.

For example, you might want to see how a disease-associated region or gene has evolved in related species.

More specifically, use CGV to find:
    • chromosome rearrangements, such as inversions
    • large-scale insertions or deletions
    • blocks of synteny, such as gene order conservation, between different species
    • gene duplications or gene loss
    • genomic changes in older and newer assemblies for the same species, or between different strains of the same species

What can CGV do?

    • Compare two eukaryotic assemblies
          CGV includes animals, plants, and fungi
      • > 400 assemblies
      • ~200 species
      • ~480 alignments

            And continues to grow!

          CGV does not include mitchondrial genomes.


        • Different assemblies for the same organism


      Two honey bee assemblies


        • Cross-species comparisons

    • Ideogram view of arctic fox and labrador retriever


    • View as a dotplot

    • Dotplot view of arctic fox and labrador retriever


    • View chromosomes → genes → sequence
      • View at the gene level

    • Zoomed in to level with gene structure, and gene histogram labeled


      • View and analyze at the sequence level four ways
    • (This is an image of the pop-up you get when you right-click on an alignment)


      Pop-up showing links to MSA viewer, GDV, etc.


    • Download a graphics file of the current view
    • Download alignment files
    • Request alignments
    • Help documentation


      Image from Help about how to navigate


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Last Reviewed: July 12, 2023