Console application to redesign mRNA nucleotide sequences (given as text strings) to enhance its secondary structure in terms of minimum free energy
Usage: mRNAoptimizer [*options*] nucleotide_sequence
Example usages:
**mRNAoptimizer** GUCACGUACUGACGUACUGCAGUCA
**mRNAoptimizer** -f sequence_file.txt
**mRNAoptimizer** -f sequence_file.txt -b 100 -e 300 -o output.txt
Options:
-
-f inputFile
Give input sequence as a file. -
-o outputFile
Output results to file (Default = standard output). -
-b index
Index of the first nucleotide of the start codon (default=1) -
-e index
Index of the last nucleotide of the stop codon (default = sequence size) -
-d type
Optimization type: 0 to maximize MFE (default) / 1 to minimize MFE -
-t maxTime
Maximum optimization time, in minutes (default = no limit). -
-i iterations
Number of iterations the algorithm runs. The more iterations the longer it will take, but results will usually be better (default = 4000) -
-c codingTable
Genetic Code Table to use(default=1) according to this list: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi -
-q
Don't output anything else than the resulting sequence. -
-g
Maintain the same GC content as the original sequence. With this option, the MFE optimization won't be as expressive.