A new tool has been added to Proksee:

Genome Loom

• Create comparative genome ribbon plots from a reference genome and one or more comparison genomes.
• Visualize conserved sequence blocks, rearrangements, inversions, missing regions, and assembly fragmentation across related genomes.
• Generate several complementary views from the same analysis.
• Download figure outputs and summary metadata for downstream review.

Genome Loom adds a ribbon-based view for comparing genome structure. It follows aligned regions from a reference into related assemblies, making it easier to see shared sequence context, inversions, rearrangements, assembly breaks, and regions that are present in some genomes but absent in others.

The available views are:

• Overview: shows the reference genome aligned to all comparison genomes in one stacked figure.
• Neighbor-chain: shows ribbons only between adjacent rows in the selected genome order, making stepwise relationships easier to follow.
• All-pairs: creates two-genome figures for every selected pair, including pairs that do not include the reference.

The examples below use a compact E. coli-derived reference region with two closely related synthetic variants. One variant contains a local inversion, and the other has a deleted/reordered segment. The reference is divided into ordered color segments so that sequence position can be followed through the ribbons.

Overview view showing the reference, an inversion variant, and an island-loss variant in one stacked figure.

Reference-pair view showing a local inversion as a crossing ribbon between matching reference segments.

Reference-pair view showing gaps where reference segments are absent or no longer contiguous in the related genome.

Genome Loom uses minimap2-based alignments and works well for compact genome comparisons, including plasmids, organellar genomes, and bacterial chromosomes. It can be used as a quick visual check before deeper analysis, as a figure-generation step for comparative genomics projects, or as a way to communicate structural differences among closely related assemblies.