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Exploring the Relationship Between Two Eukaryotic Genomes Using the Comparative Genome Viewer

Wayne Matten, PhD

Workshop Duration:  2 hours

Content Difficulty:  Beginner

Target Audience:

This workshop is designed for any life scientist, including research students and educators, who want to visually compare genomes to gain biological insight and share these insights with others.  Some familiarity with genomics vocabulary and concepts is recommended for attendees.

Workshop Description:

The Comparative Genome Viewer (CGV) is a visualization tool that helps you quickly compare two genomes based on assembly-assembly alignments provided by NCBI. CGV includes eukaryotic (animal, plant and fungal) assemblies, and many cross-species comparisons. You can view chromosome-scale rearrangements, search for genes, and display aligned regions at the sequence level.

In this workshop, you will have the opportunity to:

  • Compare the human T2T CHM3 assembly to the current reference assembly, GRCh38.14
  • Explore the extent of gene order conservation (synteny) between two organisms
  • Transfer a viewed region to the Genome Data Viewer where you can expand your analysis
  • View pairwise alignment at the sequence level
  • Download a FASTA alignment file for a region, or download complete whole genome alignment data
  • Generate a scalable vector graphics image (SVG) of your current view

Data Access Technology:  NCBI Website

NCBI Resources: 
Comparative Genome Viewer, Genome Data Viewer

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Last Reviewed: May 18, 2023