This repository uses RiboTree-mRNA to optimize our mRNA sequences. However, the files related to RiboTree have been omitted from the repository since the tool is distributed with a license. The following sequences have been optimized.

1. Anti PD1
2. Anti PD1 nanobody
3. Q-IL6-9 antibody
4. Q-IL6-9 nanobody
5. O-IL8-15 antibody
6. O-IL8-15 nanobody
7. CD36

Some additional things to install

$ sudo apt-get install gfortran
$ sudo apt-get install liblapack-dev liblapacke-dev
$ pip install setuptools networkx matplotlib scipy numpy pandas

Arnie File

#Path to EternaFold
eternafold: /path/to/mRNA-Optimization/eternafold/src

# Vienna RNAfold 2 Linux build from source:
vienna: /path/to/mRNA-Optimization/ViennaRNA-2.6.3/src/bin
vienna_2: /path/to/mRNA-Optimization/ViennaRNA-2.6.3/src/bin

# CONTRAfold build
contrafold_2: /path/to/mRNA-Optimization/contrafold-se/src

# LinearFold build
linearfold: /path/to/mRNA-Optimization/LinearFold/bin

#LinearPartition build
linearpartition: /path/to/mRNA-Optimization/LinearPartition/bin

#directory to write temp files
TMP: /tmp

---

Open-source Contributions

Open PRs

1. Fixed InferenceEngine.hpp in contrafold-se

Merged PRs

1. Modify documentation for adding Vienna to arnie file in arnie
2. Fixed error with file deletion on first run in arnie

Other bugs reports

1. Deprecated pandas method in RiboTree-mRNA