TransSite

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.

installation

pip

pip install -i https://test.pypi.org/simple/ transsite --target=/path/where/to/install/ transsite && cd transsite

conda

conda install transsite

docker [TODO]

usage

single protein:

transsite.py <protein> <ref> <position> <mut>
   
 e.g. 
   
transsite.py Lactb M 1 S

input file:

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>)

output

<protein> <mutation-position> <charge-difference> <molecular-weight-difference> <substitutaion-score> <conservation-score> <prediction>

contact:

if you run into any problem do raise an "issue", also see wiki for proper use and parameters or contact at aarslan@stanford.edu

Read more:

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