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.  

Continue reading “Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily” →

Easily distinguish reverse orientation alignments

We are excited to announce an update to NCBI’s Comparative Genome Viewer (CGV) that allows you to quickly determine the relative orientation of aligned segments. CGV displays whole genome alignments between two different eukaryotic assemblies (Figure 1). 

In the viewer, individual alignment regions are connected by colored bands between two chromosomes. These alignments are now colored differently depending on whether the aligned sequences on the two assemblies are in the same orientation (forward) or reverse orientation relative to one another. Forward orientation alignments are connected by green bands, whereas reverse alignments are connected by purple bands. Reverse alignments represent local genome inversions or inverted translocations and may point to areas of significant biological difference between the two assemblies.   Continue reading “New feature in the Comparative Genome Viewer!” →

New search feature in the Comparative Genome Viewer (CGV)

You asked, we listened! We are pleased to announce that you can now search for a gene in NCBI’s Comparative Genome Viewer (CGV) and navigate directly to its location in the viewer.

Maybe you’re studying a particular gene or gene family, and you want to see if that gene is annotated in the assemblies you’re viewing. Or maybe you know that a gene is annotated on one of the assemblies, but you want to obtain the coordinates of the aligned region on an unannotated assembly. These coordinates may help you find the ortholog for the gene in the aligned assembly.

To start, simply enter a gene symbol, name, or description in the search box at the top of the alignment in GDV and click ‘Search’. Continue reading “Find your favorite gene in aligned assemblies!” →