Splicing^Lab

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

User interface

Input

A single sequence, DNA or RNA

Output

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.

About

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.

• This notebook is modeld after the ColabFold notebook.