A Google Colab notebook/web server for predicting tissue-specific splice site usage from a single sequence using Pangolin
Analyze your own sequence here: https://colab.research.google.com/github/xuebingwu/SplicingLab/blob/main/splicingScan.ipynb
A single sequence, DNA or RNA
A figure and a table for predicted sites on both strands. Output files will be zipped and downloaded. See below the output when using ACTB pre-mRNA as input.
Applications
- Identify potential splicing artifacts in plasmid reporters.
Limitations
- A gmail account is required to run Google Colab notebooks.
- This notebook was designed for analyzing a single sequence.
- Only sequences of length 1-150,000 bases have been tested. Longer sequences may fail due to a lack of memory.
- The first run is slow due to the need to install the
Pangolin
package. - GPU may not be available and running the prediction on CPU will be significantly slower.
- Your browser can block the pop-up for downloading the result file. You can choose the
save_to_google_drive
option to upload to Google Drive instead or manually download the result file: Click on the little folder icon to the left, navigate to file:res.zip
, right-click and select "Download".
Bugs
- If you encounter any bugs, please report the issue by emailing Xuebing Wu (xw2629 at cumc dot columbia dot edu)
License
- The source code of this notebook is licensed under MIT. See details of the license for Pangolin here.
Acknowledgments
-
We thank the Pangolin team for developing an excellent model and open sourcing the software.
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This notebook is modeld after the ColabFold notebook.