Follow some typical use-cases to learn how to use GenomeHubs in your research. Each tutorial uses a specific GenomeHub as an example but should be applicable across all community GenomeHubs. Click the headers below to find out more.
Each GenomeHub has three subdomains where the main tools can be found:
ensembl. For MealyBugBase (mealybug.org), these are blast.mealybug.org, download.mealybug.org and ensembl.mealybug.org.
Search with a sequence
If you already have the sequence for a gene that you are interested in, use the
blast. subdomain to identify homologous genes or regions across all assemblies in a GenomeHub.
Search by functional annotation
Each assembly in a GenomeHub is decorated with functional annotations based on BLAST and InterProScan analyses. Use the search box on one of the assembly pages under the
ensembl. subdomain to perform a keyword search and find genes by predicted function.
Jump to a specific location
If you already know the region of an assembly that you are interested in, type a query of the form
scaffold_name:start-end into the search box in the
ensembl. subdomain to jump directly to that location in the genome browser.
View orthologues and gene trees
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.
Explore additional tracks
Additional tracks (e.g. RNASeq coverage across the genome) may be displayed for assemblies by configuring the
location view in the
ensembl. subdomain. The availability of these data depends on appropriate TrackHubs being loaded by the site curator.
Download bulk datasets
Bulk file downloads for all sequence and analysis files are made available under the