/Pred_CIS

使用MEME软件预测基因组顺势调控元件

Primary LanguagePythonMIT LicenseMIT

Pred_CIS: Cis-Regulatory Element Prediction Script

This script is designed to predict cis-regulatory elements in a genomic sequence using the MEME software. It processes the output from MEME, extracts relevant information, and writes the results to a text file.

Prerequisites

Before running this script, make sure you have the following installed:

These libraries are part of the Python Standard Library and should be available with Python installation.

Usage

  1. Place your genomic DNA sequence file in the same directory as the script. The file should be in FASTA format.

  2. Modify the genome_file variable in the script if your genome file is named differently than the default genome.fa.

  3. Run the script using Python:

    python cis_regulatory_element_prediction.py
    

Output Format

The output file cis_elements.txt contains the following columns separated by tabs:

  • Start position of the cis-regulatory element in the genome sequence.
  • End position of the cis-regulatory element in the genome sequence.
  • The DNA sequence of the cis-regulatory element.
  • Each line in the file represents a single predicted cis-regulatory element.

Troubleshooting

If the MEME command fails or the expected output file is not found, the script will terminate with an error message indicating what went wrong. Ensure that MEME is correctly installed and accessible from your command line.

If there is a mismatch in the number of start positions, end positions, and sequences extracted, the script will also terminate with an error message. Check the MEME output files for any inconsistencies.

License

Specify the license under which this script is released, if applicable.

Contact

For any questions or issues, please open an issue on the GitHub repository or contact the maintainer directly.