SpliceSight

Frequently Asked Questions (FAQ)

1. What is this tool?

This tool is a web-based application that allows users to input genetic variants and visualise the splicing scores produced by SpliceAI. The scores are displayed in an integrated genome viewer (IGV) track format, providing an intuitive way to interpret potential splicing effects of the variants.

2. How do I input a variant into the tool?

Simply enter the variant information into the search box provided on the homepage. You can input the variant using the following formats:

  • HGVS notation (e.g., NM_021146.4:c.477+1G>A)

Once you submit the variant, the tool will retrieve the corresponding SpliceAI scores and display them on an IGV track, allowing you to explore the potential splicing impact of the variant.

3. How are SpliceAI scores visualised?

Once a variant is submitted, the tool displays the SpliceAI scores in an IGV (Integrated Genome Viewer) track. This visualisation includes:

  • Color-coded splicing predictions with scores for donor and acceptor gain/loss.
  • Genomic context, showing exons, introns, and splice junctions around the variant.
  • Interactive features that allow you to zoom in and out on regions of interest and click on specific features for detailed information.

4. What is SpliceAI and how does it work?

SpliceAI is a deep learning-based model developed by Illumina that predicts splicing events based on DNA sequence information. The model identifies potential splice junctions or changes in splicing patterns caused by genetic variants, which may be associated with diseases or other genomic changes. Learn more about SpliceAI here.

5. Is this tool open source?

Yes, this visualisation tool is open source and complies with the GNU General Public License (GPL), the same license under which SpliceAI is released. You are free to use, modify, and redistribute this tool under the same license. You can access the code and contribute to the project through our GitHub repository.

6. What is the GNU General Public License (GPL)?

The GNU General Public License (GPL) ensures the freedom to run, study, share, and modify the software. If you modify or redistribute this tool, it must remain under the GPL to ensure others have the same rights. More details about the GPL can be found here.

7. Are there any system requirements to use the tool?

This tool works on any modern web browser, such as:

  • Google Chrome
  • Mozilla Firefox
  • Microsoft Edge
  • Safari

No software installation is required; all you need is a stable internet connection.

9. Can I export the visualisations?

Yes, you can export the IGV track visualisations as high-resolution SVG image for use in research papers, presentations, or reports. Look for the "Save SVG" button on the IGV track. (Note: This button will only appear once you have queried a variant)

10. Where can I get technical support?

For technical support, you can open an issue on our GitHub repository. Alternatively, you can click the "Feedback" button at the top.

11. Can I request additional features?

Yes, we welcome feature requests! You can suggest new features or improvements via our GitHub repository.

12. How do I cite this tool in my research?

If you use this tool in your research or publications, please cite it as follows:

"SpliceSight v0.0.84 (SpliceAI 1.3.1, Gencode 38), Available at https://splicesight.frontiergenomics.com.au, Date Accessed January 15, 2025."

Additionally, please cite the original SpliceAI paper:

Jaganathan, K. et al. Predicting Splicing from Primary Sequence with Deep Learning. Cell, 2019.

13. Who developed this tool?

This tool was developed by Peter Kneale and Himanshu Joshi from the Kids Neuroscience Centre, and builds upon SpliceAI from Illumina. We acknowledge the open-source contributions from both the SpliceAI team and the broader software community that helped make this tool possible.

14. Which assembly/transcript is being currently used for SpliceSight?

At present, SpliceSight is using: