predicting the change in protein transport-sequence activity upon the presence of genetic variations.
The presence of single residue mutations in the protein localisation peptides have not discussed or analysed at length. We have created a python code,
that take into account the change in the biochemical properties (including charge), molecular weight and isoelectric pointm the factors most important
in the protien transportation, and provide a collective change value in these parameters in a simple yet effective way.
pip install -i https://test.pypi.org/simple/ transsite --target=/path/where/to/install/ transsite && cd transsite
conda install transsite
transsite.py <protein> <ref> <position> <mut>
e.g.
transsite.py Lactb M 1 S
Lactb M 1 R
Lactb2 M 2 S
Lsr G 10 C
(tab sepated file with the same format as the single protien entry i.g. <protein> <ref> <position> <mut>)
<protein> <mutation-position> <charge-difference> <molecular-weight-difference> <substitutaion-score> <conservation-score> <prediction>
if you run into any problem do raise an "issue", also see wiki for proper use and parameters or contact at aarslan@stanford.edu
Paper is under write up, here is the latest version: Protein Cargo Assessment through Residue Alterations. Ahmed Arslan. bioRxiv 2020.11.20.387738; doi: https://doi.org/10.1101/2020.11.20.387738