Get a High-Level View of Assembly-Assembly Alignments
New feature! We added an alternate view in the Comparative Genome Viewer (CGV) that shows a dot plot (also known as a 2D plot) comparing two related genome assemblies. This added view provides a high-level overview of the assembly-assembly alignment. Dot plots help you find large genome rearrangements such as translocations or segmental duplications more easily.
Using the Dot Plot View
- From the main CGV view, you can access the dot plot by clicking on the new ‘Go to dot plot view’ link.
- Click on a cell in the plot to zoom to a pairwise comparison between two chromosomes.
- You can return to the main CGV view by clicking on ’Go to ideogram view’.
- When you return to the ideogram view from the chromosome level dot plot view, you’ll see the same chromosomes you were looking at in the dot plot. Here, you can zoom further to investigate gene annotation and obtain alignment details.
Figure 1: An example of a dot plot between assemblies for the Norway rat (mRatBN7.2) and black rat (Rrattus_CSIRO_v1). Norway rat chromosomes are plotted on the X axis. Black rat chromosomes are plotted on the Y axis. Dots or lines represent locations of assembly alignment; alignments in the same orientation are green, while those in the reverse orientation are graphed with an opposite slope and are colored purple.
Learn more
Learn how to use the CGV dot plot! For more information about CGV and for step-by-step instructions on how to use it, check out our help documentation.
Stay up to date
CGV is a part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.
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Questions?
If you have questions or would like to provide feedback, please reach out to us at [email protected].
The new feature of Comparative Genome Viewer (CGV) called the Dot Plot View is a great addition to the tool. It provides a high-level overview of the assembly-assembly alignment and helps you find large genome rearrangements such as translocations or segmental duplications more easily. The dot plot view is accessible by clicking on the new ‘Go to dot plot view’ link from the main CGV view. You can also zoom further to investigate gene annotation and obtain alignment details. This feature is especially useful for researchers who are interested in studying genome evolution and comparative genomics.
Michael Wichkoski