Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily

Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily

We are excited to introduce a new user-validated feature in the Comparative Genome Viewer (CGV) making it easier for you to analyze inverted regions. You can flip the orientation of one of the aligned chromosomes in the view, so the sequence and gene order is facing the same direction for both assemblies.  

What’s new?

When looking at genome alignments in CGV, you may find related sequence regions that are inverted in one assembly relative to another. It may be difficult to tell if gene synteny (order and orientation) is conserved in these inverted segments because the relative gene order is reversed.  

Now available! Look for the “flip” button on the left side of either the top or bottom chromosome (Figure 1).   

  • Clicking on the “flip” button will reverse the direction of the chromosome.  
  • Reverse-orientation alignments will still show up as purple but will have an “un-twisted” style.  


Check out the example below to see the flipped view of a comparison between cat and dog assemblies–the genes in the syntenic block are now ordered in the same direction. This makes it easier to see any genes that are annotated in one assembly, but unannotated or missing from the other assembly. One such gene (LOC102902067 in the example) is missing from the dog annotation.  

Figure 1. Aligned regions of the cat and dog assemblies showing a relative inversion. In the normal view (A) it may be difficult to see that synteny is conserved because the genes are annotated in the opposite order on the two assemblies. The flipped view (B) changes the twist-tie form of the graphic and shows the genes in the same order and orientation on both assemblies. In the zoomed-in view (C), it is easy to identify LOC102902067 as an annotation on the cat assembly that is absent from the dog annotation.  


If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov or click on the feedback button on the CGV page.   

Stay up to date

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. Join our mailing list to keep up to date with CGV and other CGR news. 

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