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.
This example searches for genes matching “wingless” in Heliconius erato lativitta on LepBase.
1. Visit ensembl.lepbase.org and click on the Heliconius erato lativitta assembly:
2. Use the search box at the top right to search for genes matching “wingless”:
3. As you type, autocomplete suggestions will be listed below the search box. For this example, press enter to search for “wingless”:
4. Three results are found for “wingless”. No exact matches were found so the search term has been auto-expanded to match entries with text before and after the search term – this is shown by the “%” symbols either side of the original query in the Search term box. Each search result shows the gene name and description and include direct links to the location, transcript(s) and translation(s) for that gene:
5. The match was not contained in the gene name or description so to see which entries matched your search term click the toggle external references checkbox just above the first result. This shows that the search term was found in an InterPro annotation:
6. Click the gene name for the first search result to see the gene HEL_010764 in the genome browser:
7. This view includes a transcript table which shows more information and includes a link to a protein view. Click the “186aa” link under the protein heading in the transcript table to view a Protein summary that shows the distribution of protein domains:
8. To see more information on the functional annotations, click the “General identifiers” link under External References in the menu on the left-hand side of the page. This shows a table of all external references for the gene, based on InterProScan and BLAST analyses:
9. Click “view all locations” to see all locations that have been annotated with the same InterPro domain (in this case only one gene matches):
10. Switch to the Transcript view using the grey tabs at the bottom of the page header:
11. The set of BLAST buttons just below the transcript table allow link out to blast.lepbase.org and pre-populate the query field with the Transcript, cDNA, CDS or Protein sequence ready to search for similar sequences in other assemblies (see the Search with a sequence tutorial):
12. If a comparative analysis is available, the Gene tab provides an alternative way to find related genes in other assemblies by exploring pre-computed orthologues and paralogues. See the View orthologues and gene trees tutorial for more information.