Hercules: synthetic biology

Hercules is a must-have app for all biologists, genetic engineers and biochemists.
What is Hercules?
It is an advanced, fast, modern and slick tool designed to maximise protein production from recombinant expression experiments. It optimises protein expression and solubility while providing many helpful insights and descriptions about the sequences. Currently, E. coli is the supported host. Other hosts may be included in the future.
What Hercules is not?
It is not one of those introductory educational apps with definitions and explanations of things with pretty pictures. Sorry. If nothing here made sense to you, I'd recommend using a search engine to know more about these features. I support limited queries related to app and crashes via email.
Features:
- mRNA and protein features
Several mRNA features such as Codon Adaptation Index (CAI), tRNA Adaptation Index (tAI), G C content, protein hydrophobicity, flexibility and solubility are calculated. A profile plot of these features along the sequence is also displayed. All of the sequences are automatically checked for signal peptide using the 'Razor' service from https://tisigner.com. Many of the features work completely offline.
- Prediction and optimisation of mRNA expression.
This can be done by either using the conventional methods of maximising Codon Adaptation Index (CAI, Sharp and Li (1987)), tRNA Adaptation Index (tAI, Sabi et al. (2017)) and minimising G C content or a modern approach by tuning the accessibility of translation initiation site. A powerful, inbuilt multiobjective optimisation algorithm is used to optimise the sequence using the conventional method, whereas, TIsigner service from https://tisigner.com is used to optimise the sequence using a modern approach.
- Prediction and optimisation of protein solubility
This is done using the Solubility-Weighted Index (SWI, Bhandari et al. (2020)), a recent, fast and accurate method of predicting protein solubility. Hercules has an inbuilt optimisation algorithm to optimise the solubility of the protein sequence.
Other small features:
- Translation, complement, reverse complement and oligo melting temperatures calculation. These features might be useful for planning Polymerase Chain Reaction (PCR) experiments.
- more to come ...
Please note:
- Please read the 'Help' inside the app, if you are unsure about these features.
- There are absolutely no ads in this app, despite the play store saying 'Contains ads'. This is due to the expo SDK using Facebook's Audience Network, although the app has no code to even call the library.
- Since many of the features are computed locally, the app may lag noticeably in older phones with low processing power. Sorry about that ;)
Known issues:
-File saving feature may cause the app to crash on newer Android devices (Android 11) due to a change made by Google regarding external storage. I am working on a fix for this issue.
Open source?
- To discourage the kangers, this project is currently close sourced. However, If the tool gets some traction, I am more than happy to open source the project in nearby future. I love open source as much as you do and all of my work so far is open-sourced.