Bioinformatique : cis-regulating TFBS searcher 🧬🔬

Description 📝 :

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.).

Project tree 🌲 :

├── README.md          
│
├── data
│    ├── motifs         
│    └── sequences     
│
├── src
│    ├── utiles.py
│    ├── pwm.py
│    ├── putative_TFBS.py
│    └── scan_pwm.py
│
│       
└── test.sh

Getting started 🚀 :

Before cloning the project into your local disk, please check the requierments.

Requierments 🧾 :

python 3.8
valide SSL CERTIFICATE for python
biopython

Usage 💻 :

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

Autors ✏️ :

AMRI Anes Saad Eddine.