Find your favorite gene in aligned assemblies!

Find your favorite gene in aligned assemblies!

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’.

The ‘Search results’ table (Figure 1) reports genes matching your search term sorted by assembly. If there’s a perfect match for your search term, you’ll be automatically taken to the location in the viewer.

If there are multiple matches, you can hover over a row to select the result of interest. When you select a search result, the viewer will go to the location on the selected assembly, as well as to the aligned region on the other assembly.

Figure 1. Search results for ‘Pax’ in CGV for the alignment of the Mus caroli CAROLI_EI)J_v1.1 and Mus musculus GRCm39 assemblies. Clicking the Pax6 location loads the view shown in Figure 2.

In Figure 2, the Pax6 gene in Mus caroli and its ortholog in Mus musculus are both found in an assembly-assembly alignment (indicated with red boxes).

Once you’ve found the region of your gene, you can also zoom out to see if synteny is conserved in the gene neighborhood. You may discover other differences that may be biologically interesting, such as at the star in the image below, which shows a gene annotated in Mus musculus that is not annotated in Mus caroli.

Figure 2. Aligned Pax6 region of the Mus caroli CAROLI_EI)J_v1.1 and Mus musculus GRCm39 assemblies in CGV showing the Pax6 orthologs (red boxes) in each assembly. The annotated Rpl10 pseudogene 1 (red star) is not annotated in the Mus caroli assembly.

Check out our documentation  and our previous post for more information on how to get the most out of CGV. We’re continuing to add new features and alignments. If you have any requests, please click on the Feedback button at the bottom of the page and let us know!

CGV supports 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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