Promoter Architecture Scanner

Promoter Scanner is a tool designed to segment and align promoter elements upstream of TSS in bacteria. Detailed algorithms and methodologies are provided in the accompanying article.

In this article, we used various bacterial genomes listed in Genome_List.csv. Their GenBank files are located in the genomes folder. The TSS-mapping data we collected is provided in the TSS_List.tsv table. The segmentation results are in the tables folder.

To reproduce the results presented in the article, run the following Python script:

python scripts/scanner_multiprocessing.py

If you wish to use your own data, replace the TSS_List.tsv file with your data and place the corresponding genome GenBank files in the genomes folder.

Environment

The required environment is specified in environment.yml. To set up the environment using conda, run:

conda env create -f environment.yml

Citation

Unraveling the start element and regulatory divergence of core promoters across the domain Bacteria

License

© 2024 David Chou Lab, Department of Life Science, National Taiwan University

Contact Information

For any inquiries, please contact:

Antony Kuo
Email: antonykuo@ntu.edu.tw

David Chou
Email: chouhh@ntu.edu.tw