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.
Figure 1. Alignment of one chromosome of Brassica napus Brassica_napus_assembly_v1.0 (GCF_000686985.1) (top) and the whole genome of Brassica napus Bra_napus_v2.0 (GCF_000686985.2) (bottom) showing aligned regions that are in the same orientation (green bands) and aligned regions in the relative reverse orientation (purple bands).
In addition, bands representing reverse alignments also show a twisted (twist-tie) form when you zoom in, indicating the reversal in orientation (Figure 2).
Figure 2. Close-up view of a reverse orientation alignment between segments on two assemblies (Brassica_napus_assembly_v1.0 (GCF_000686985.1) (top) and Bra_napus_v2.0 (GCF_000686985.2) (bottom)). The twisted blue band indicates a relative inversion in the aligned segment.
You can choose to simplify your view to show only forward or reverse alignments using the options located under the comparative viewer. These options allow you to find areas of significant genome rearrangements more easily and quickly.
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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.
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