Transcript sequences for Pythia_Webtool_V1

This dataset contains pre-built transcript sequence databases for Homo sapiens, Mus musculus, and Xenopus tropicalis, derived from Ensembl/Xenbase annotations. These databases enable the auto-fill functionality of Pythia’s Custom Tagging tool, allowing users to select a gene and transcript isoform and have the relevant target and flanking genomic sequences populated automatically without manual sequence input.

The transcript databases are required for full local functionality of the Pythia web interface when installed via the conda route. They are already bundled inside the official Docker image (thomasnaert/pythia_webtool:v1.0.0) and do not need to be downloaded separately when using Docker.

Companion datasets containing the genome-wide precomputed Pythia predictions (used by the Pre-calculated Tagging browser) are available on Zenodo as separate records for Homo sapiens (exonic and intronic), Mus musculus, and Xenopus tropicalis.

Source code and documentation: https://github.com/XenoThomasNaert/Pythia_Webtool

Associated publication: Naert et al. Nature Biotechnology (2025), doi:10.1038/s41587-025-02771-0. A companion protocol paper is currently under revision; this record will be updated upon acceptance.

Please cite the associated publication when using this dataset.