NLM’s NCBI is introducing the Comparative Genome Viewer (CGV), an easy-to-use visualization tool that helps you quickly compare eukaryotic genome assemblies and easily identify genomic changes that may be significant to biology and evolution. With the new CGV you can view and compare the alignment between two assemblies to see differences in genomic sequence and structure, including deletions, inversions, and translocations. Currently, you can compare assemblies from over 50 annotated animal and plant genomes.
You can view assembly-assembly comparisons at the whole genome (Figure 1), chromosome (Figure 2), or chromosome region (Figure 3) levels.
Figure 1. CGV full genome comparison view of two zebrafish (Danio rerio) assemblies. Colored bars represent aligned regions and reveal that there are numerous genome rearrangements between these two assemblies. You can view this example here. 
Figure 2. CGV chromosome-level view comparing chromosomes 3 of Drosophila miranda and Drosophila pseudoobscura. Colored bars indicate that there are multiple inversions between the genomes of these two species. You can view this example here.
Figure 3. CGV view of a region containing a relative inversion between the human GRCh38 assembly and the recent T2T-CHM13v2.0 assembly. An assembly-assembly alignment block is highlighted in blue. The information box reports that the relative orientation is in reverse (suggesting an inversion) and provides access to viewing more details in NCBI’s Genome Data Viewer (GDV) browser. The annotated HYDIN2 pseudogenes are highlighted on the two assemblies and show that the gene order in this region is opposite. View this example here.
We want to hear from you!
We will update CGV based on your feedback. Try out our new tool and let us know what you think! In the coming months, we will add new features, including more cross-species alignments. Please contact us if you’d like us to add specific alignments and, of course, to provide other feedback!
The CGV is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms.
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