If orthology predictions are available for the assemblies in a GenomeHub, sets of orthologous and paralogous genes and gene trees based on these sets can be accessed from a gene page in the ensembl. subdomain. These data are added to a GenomeHub based on an OrthoFinder analysis of the imported assemblies and may not be made available until some time after the initial release of a GenomeHub.
This example finds orthologues and paralogues of Bicyclus anynana gene BANY.1.2.b04016 in LepBase.
1. Follow the link to Bicyclus anynana gene BANY.1.2.b04016:
2. Click on the “Gene tree” button below the transcript table or the “Gene tree” link under Lepidopteran compara in the menu on the left-hand side to view a gene tree:
3. Collapsed nodes are shown as grey triangles. To expand a collapsed node, click on the square at the node to bring up a menu and select “expand this sub-tree”:
4. To go directly to one of the genes in the gene tree, click on the gene name (e.g. RR48_04951 Papilio machaon) to bring up a menu with further information including a link to the gene:
5. The linked gene page contains the same set of links to gene trees and the Lepidopteran Compara as the original Bicyclus anynana BANY.1.2.b04016 gene page:
6. Click the “Orthologues” link under Lepidopteran compara in the menu on the left-hand side to view a table of orthologous genes:
7. Or the “Paralogues” link to view a table of paralogous genes:
8. Clicking on the “Alignment (protein)” links under the Compare heading in either the Orthologues or Paralogues table shows a pairwise alignment of the two genes:
