RiboMaker Files

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| RiboMaker |
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Developed by Guillermo Rodrigo

RiboMaker is licensed under a free Creative Commons Attribution-Noncommercial 3.0. License (http://creativecommons.org/licenses/by-nc/3.0). 
If you use this software for your research, please provide the appropriate reference to this work. 

RiboMaker is a C++ program aimed at the automatic design of riboregulators (sRNAs) and 5' untranslated regions (5'UTRs) to control gene expression.

For compiling
g++ -c -g -Wall -O4 RiboMaker.cc -I$Path_to_ViennaRNA/include/ViennaRNA
g++ -o RiboMaker RiboMaker.o -L$Path_to_ViennaRNA/lib -lRNA -lm

For executing
./RiboMaker FILE ID ITER SUBITER TEMP

An example is ./RiboMaker riboreg_neg 0 3000 100 1

It reads the file riboreg_neg.txt, writes the file riboreg_neg.0.out, uses 3000 iterations, writes intermediate solutions every 100 iterations, and uses an initial MCSA temperature of 1. 

Examples of input files are provided: riboreg_neg.txt (for negative riboregulation) and riboreg_pos.txt (for positive riboregulation). 

Use lower-case letters to specify constant nucleotides, upper-case for initial nucleotides, and N to not specify any nucleotide. Use '.' to specify unpaired nucleotide, '|' for paired nucleotide, and '?' to not specify any structure.

Use -1 as MCSA temperature for random sampling.

In the output file, it gives the structures of the 5'UTR, sRNA and the complex 5'UTR:sRNA, together with the score.