Use cases for Tools at the Bovine Genome Database

1. Use cases for Tools at the Bovine Genome Database Apollo and Bovine QTL viewer

2. Apollo: Creating and editing annotations Apollo is a graphical annotation editor which has a robust set of functions for viewing, creating and editing annotations. The following slides cover different scenarios that annotators may encounter.

3. Apollo: Adding UTRs to a gene model To create an annotation, simply click and drag one of the gene models from the evidence panel. In this case, the OGSv1 (GLEAN) gene model is used as the basis for the annotation. Examining the cDNA data (light blue track) shows experimental evidence for UTR regions. The cDNA evidence will be used to annotate UTRs for our gene model.

4. Apollo: Adding UTRs to a gene model To adjust the 3’ end of the gene model first click on the last exon. Then shift + click on the evidence (cDNA) exon we want to use to set the 3’ end. Right click on the cDNA then click “Set as 3’ end”.

5. Apollo: Adding UTRs to a gene model The process is the same for setting the 5’ end of the gene.

6. Apollo: Splitting a gene model Some gene predictions are fusions of two genes into a single prediction. In this case, the evidence supports two genes instead of one. The gene model needs to be split into two separate gene models.

7. Apollo: Splitting a gene model The extra exon is removed by clicking on the exon, then right clicking and clicking the “Delete selection” option. This only removes the selected feature, and does not split the gene model.

8. Apollo: Splitting a gene model To break the gene into two distinct gene models, select the two exons flanking the region to split on, then right click and select “Split transcript.”

9. Apollo: Splitting a gene model The cDNA evidence supports an additional 3’ exon for the first gene model. Drag the exon into the annotation panel, then select the new exon and the last exon of the gene model then add the exon to the gene using the “Merge transcripts” feature.

10. Apollo: Splitting a gene model The removal of the second gene and the addition of the new terminal exon has altered the coding sequence of the gene. To recalculate the ORF, click on the gene then right click and select the “Calculate longest ORF.” The coding sequence should be examined to ensure correctness, and may need to be adjusted.

11. Apollo: Splitting a gene model View of the region after annotation, showing both finished gene models.

12. Apollo Merging Gene models View of a region containing two gene models with evidence supporting a merge. Both OGS gene models have been dragged into the annotation panel.

13. Apollo Merging Gene models To merge the gene models, select both genes, then right click and select “Merge transcripts.” This only connects the two gene models into a single annotation. Additional annotating is needed to correct the gene model.

14. Apollo Merging Gene models The exon boundaries need to be adjusted based on cDNA evidence.

15. Apollo Merging Gene models Add a new terminal exon to the gene model based on the cDNA evidence. Once this is complete, recalculate the longest ORF, then verify that the coding sequence is correct.

16. Apollo Merging Gene models View of the completed annotation.

17. Using the Bovine QTL Viewer The viewer is located at: http://genomes.sapac.edu.au/bovineqtl/ Users enter the site by clicking the Guest button.

18. Using the Bovine QTL Viewer The initial search page has two options for accessing the QTL data. Users may select different traits, then select the chromosomes of interest, including all chromosomes. In this example the search is for carcass quality and carcass yield, across all chromosomes. Click Submit to begin the search.

19. Using the Bovine QTL Viewer Search results. The chromosomes are listed in order, with the QTL drawn alongside the respective chromosome. Different colors are used for each type of QTL searched for. Chromosome 18 has overlapping QTL for both traits. Clicking on the chromosome will open the detailed overview.

20. Using the Bovine QTL Viewer The detailed view of chromosome 18 shows that there are several carcass yield QTL that overlap the carcass quality QTL. Clicking on eof the QTL features opens the QTL record page.

21. Using the Bovine QTL Viewer The QTL record page displays the information for the QTL feature, including trait characteristics, significance level and additional comments. There are also links to additional resources, including gbrowse and composite map viewers, literature references and links to MARC Marker reports.

22. Using the Bovine QTL Viewer The QTLs may also be searched directly by using the search box on the right side of the page. In this example the trait “Foot Angle” is being searched for, with the limitation that only significant QTL be displayed. Click Submit to execute the query.

23. Using the Bovine QTL Viewer QTL search results, showing a summary of the QTL matching the search criteria. Clicking any of the QTL Ids will open the respective QTL record.