Codon Scrambler currently under maintenance! While we migrate the backend to a new server, if you need to create codon-scrambled DNA we recommend using IDT DNA's codon optimization tool (https://www.idtdna.com/codonopt), entering in your amino acid sequence, and using the "manual optimization" function to quickly and easily reduce codon complexity.
This supplementary code provides a MATLAB implementation of codon scrambling from the paper: "Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins" (doi: 10.1038/NMAT4521).
Web Server
Available here: public-beta, version 1.0.
Contents
There are 2 main functions :
1) codon_scrambler.m
2) calc_obj.m
The function "codon_scrambler.m" is used for codon scrambling of tandem-repetitive amino acid sequences, interspersed-repeat amino acid sequences, or other semi-repetitive amino acid sequences.
The function "calc_obj.m" is used to calculate the objective value of a nucleotide sequence.
Requirements
The code makes use of CPLEX ILOG software (https://www-304.ibm.com/ibm/university/academic/pub/jsps/assetredirector...), UNAFOLD (http://homepages.rpi.edu/~zukerm/download/UNAFold_download.html or http://unafold.rna.albany.edu/?q=DINAMelt/software), and MATLAB's Bioinformatics and Statistics toolboxes. They should be installed.
This has only been tested on the Windows and Linux x64 platforms. Use the MATLAB command, "mex mexLRS.cpp", to compile "mexLRS.cpp" used in the "calc_obj.m" function.
The UNAFold and CPLEX directories should be edited for your system by modifying "load_preferences.m".
The code was written by Nicholas Tang at Duke University, USA.