NCBI's Comparative Genome Viewer (CGV), allow you to view the alignments between two assemblies to see differences in genomic sequence and structure, including deletions, inversions, and translocations. Currently, you can compare assemblies from over 50 annotated animal and plant genomes. Example: Mus caroli CAROLI_EIJ_v1.1 (GCF_900094665.1) and Mus musculus GRCm39 (GCF_000001635.27).
The latest update allows you to search for a gene in NCBI’s Comparative Genome Viewer (CGV) and navigate directly to its location in the viewer and compare orthologous regions in the aligned assemblies. Details at NCBI Insights. Please try it out and let us know what you think.
PeterC_NCBI nice viewer.
How were the alignments generated? I don't think I saw any specifics on help page. I am also curious as to how the alignment block size adjustment slider works. Surely alignments were not done at different block sizes.
GenoMax The development team says that the slider is a filter that determines the minimum size of the alignments that are shown in the viewer. It's not a reflection of the underlying alignment. The alignments are mostly generated by Remap as the documentation suggests.
Thanks for asking. Here is some documentation on how the alignments were made. But that doesn't address your question about block sizes. Let me get some details from the development team.