TISIGNER web app

TISIGNER (tie-SIGN-er) runs at https://tisigner.com, which includes TIsigner, SoDoPE and Razor, the protein expression optimisation, solubility optimisation and signal peptides prediction tools, respectively.

This is a reimplementation of TISIGNER in ReactJS, with more features and smoother integration between the biological sequence optimisation tools. The source code for the older website can be found here.

Installation

Requirements

• Python v3.6.9 and optionally git.
• Node.js v8.10.0. See instructions on the Node.js website.
• ViennaRNA v2.4.11. Newer versions may also work. See instructions on the ViennaRNA website.
• INFERNAL v1.1.2 . Newer versions may also work. See instructions on the INFERNAL website.

Note

If you are on a higher node version, you can follow these steps:

sudo npm install -g n
sudo n 8.10.0

Download the source and extract to a folder. If you have git installed, please run the following commands:

$ git clone https://github.com/Gardner-BinfLab/TISIGNER-ReactJS.git

Download the LazyPair models from here and run the following commands:

$ gunzip lazypair_clfs.pickle.gz
$ mv lazypair_clfs.pickle models.pkl
$ mv models.pkl TISIGNER-ReactJS/models/scallion/
$ cd TISIGNER-ReactJS/

Once you are in the source code directory, run the following commands:

$ npm install
$ npm run build

You may want to install the python dependencies on a venv. This can be done by the following commands:

python3 -m venv env
source env/bin/activate

Then you can run the following commands to activate the backend:

$ pip install -r requirements.txt
$ python3 tisigner.py

The local website will now run at http://localhost:5050. TIsigner will run at http://localhost:5050/tisigner, SoDoPE at http://localhost:5050/sodope and Razor at http://localhost:5050/razor.

Bugs/Errors

If you found any bugs or errors, please report it to us by opening an issue!

Cite

• Lim, C.S., Bhandari, B.K., Gardner, P.P., (2022). LazyPair: scalable prediction of protein-protein interactions and interaction types. bioRxiv. DOI:10.1101/2022.02.21.481370
• Bhandari, B.K., Lim, C.S., Remus D.M., Chen A., Dolleweerd C.,Gardner, P.P. (2021) Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLOS Comp. Bio. DOI:10.1371/journal.pcbi.1009461
• Bhandari, B.K., Lim, C.S., Gardner, P.P., (2021) TISIGNER.com:web services for improving recombinant protein production. Nucleic Acids Research. DOI:10.1093/nar/gkab175
• Bikash K Bhandari, Paul P Gardner, Chun Shen Lim. (2020). Solubility-Weighted Index: fast and accurate prediction of protein solubility. Bioinformatics. DOI:10.1093/bioinformatics/btaa578
• Bhandari, B.K., Gardner, P.P., Lim, C.S., (2020). Annotating eukaryotic and toxin-specific signal peptides using Razor. bioRxiv. DOI:10.1101/2020.11.30.405613