Gene and Sequence tracks in Genomic Alignment Images for selected Cactus alignments will be hidden from view at medium and large scales in Ensembl Release 114.
The default view for tracks in Genomic Alignment images for selected Cactus alignments will be limited based on the scale of view in kilobases as outlined in Table 1 below. At small scales, these Cactus alignment image views will appear much like other multiple genomic alignments, with tracks showing genes and contigs mapped onto the alignment view coordinates. When a region of one of these alignments is viewed at medium scales, track visibility will be switched off for gene tracks. When viewed at large scales, sequence tracks will also be switched off.
This change applies to the following Cactus alignment views in Ensembl Plants and Metazoa for release 114. Each is listed with the threshold region lengths (in kilobases) above which gene tracks and sequence tracks (respectively) are hidden.
Edit notice June 2025 – This blog previously described visibility thresholds for species in Ensembl Vertebrates. Please note visibility thresholds have been disabled for Ensembl Vertebrates.
Table 1: Default visibility thresholds for Cactus alignment view scales
| Alignment(s) | Ensembl division | Gene track threshold | Sequence track threshold |
| Wheat | Plants | 50 kb | 100 kb |
| Drosophila pangenome | Metazoa | 25 kb | 50 kb |
Below are screenshots of the display at various scales for example purposes:
Alignment view of a subset of the 16 wheat component A Cactus alignment image at a small scale where gene and contig tracks are visible.
Alignment view of a subset of the 16 wheat component A Cactus alignment image at a medium scale where gene tracks are hidden, but contig tracks are visible.
Alignment view of a subset of the 16 wheat component A Cactus alignment image at a large scale where gene tracks and contig tracks are hidden.
Re-enabling Tracks
To unhide gene tracks, you can “Zoom in” by using the “+” icon in the zoom slider at the top right hand side of the display, or enable them directly via the Ensembl Control Panel by clicking “Configure this page” on the left hand side menu, or “Add/remove tracks”, by clicking “Genes and transcripts” in the sidebar menu of the “Configure Alignments Image” tab, selecting the “Species to configure” from the dropdown list, and clicking the checkbox of the tracks you would like to display.
Contig tracks can be enabled by clicking on “Sequence and assembly” in the sidebar of the the “Configure Alignments Image” tab:
Please note that enabling the tracks at very large scales may cause the image generation to fail due to a timeout error.
Authors: Jorge Batista da Rocha and Thomas Walsh