The project consists in solving the problem of finding cis-regulating TFBS of a set of genes.
Using the Biopython module and the interaction with the NCBI and JASPAR databases, we realized a program in python which allows to look for TFBS on a set of genes supposed co-regulated by a TF.
The method used is the sliding window, and our approach is the calculation of the distance between the occurrences (hits) of TFBS on promoter sequences (see slide.).
├── README.md
│
├── data
│ ├── motifs
│ └── sequences
│
├── src
│ ├── utiles.py
│ ├── pwm.py
│ ├── putative_TFBS.py
│ └── scan_pwm.py
│
│
└── test.sh
Before cloning the project into your local disk, please check the requierments.
python 3.8valide SSL CERTIFICATE for pythonbiopython
git clone https://github.com/Nissou31/bio-informatique.git
cd bio-informatique
./test.sh
The bash script will run automatically the program with differents settings.
To test only the putative_TFBS.py
cd src
python3 putative_TFBS.py --help
Results :
usage: putative_TFBS.py [-h] -t T [-l L] [-w W] -m M -s S [-p P] [mrna [mrna ...]]
Find the index of the best window for a TFBS.
positional arguments:
mrna list of mRNA id.
optional arguments:
-h, --help show this help message and exit
-t T, --threshold T score threshold for pssm
-l L, --promotor-length L
promotor sequence length
-w W, --window-size W
sliding window size
-m M, --pfm M jaspar matrix name
-s S, --window-threshold S
window score threshold
-p P, --pseudocount P
pseudo-count weight
- AMRI Anes Saad Eddine.