ResConservScorePy

Pipeline writen in python to get a given protein's residues conservation JSD scores

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Description :

The pipeline is the following :

• First the user gives a protein name, and the code will look in Uniprot for an ID corresponding to this protein
• Then a Blastp is run on the sequence of this protein ID using UniProtKB/Swiss-Prot database.
• A multiple sequence alignment is then proceeded using MAFFT.
• Finaly the residues conservation scores are calculated using the JS Divergence method.

Requirements :

System :

• Linux : The code has only been tested on Ubuntu.

Browser :

The code has only been tested with firefox.

Python packages :

In order to be able to run this code of course you need to have python3 but also some python packages :

• selenium
• argparse
• BioPython
• pandas

PyPi installation :

$pip install selenium
$pip install argparse
$pip install pandas
$pip install biopython

Conda installation :

$conda create -n resconsscore python
$source activate resconsscore
$conda install -c conda-forge selenium
$conda install -c conda-forge argparse
$conda install pandas
conda install -c conda-forge biopython

Others :

selenium requires geckodriver for firefox, check this link for the other browsers.

Script files :

Conservation.py Auto_Uniprot.py Blast_Align.py Auto_Mafft.py Res_Conserv_Score.py

Usage :

1. First clone this repository :

$git clone https://github.com/hocinebib/ResConsScorePipeline.git

or download it.

Exemple of usage :

$cd ResConsScorePipeline/
$python src/Conservation.py "MexA MexB OprM"