Non-coding small RNA reaction and structure calculation
============================================================================ Name : RNAgate Author : Marzuk M Kamal Version : 1.1 ============================================================================ Usage:
rnagate inputfilename.txt outputfilename.txt -OPTIONS OPTIONS must be either or both of the following: f = write to file outputfilename.txt s = write to standard output, i.e. display the results on screen r = calculate the subsequence free probability.... To write both to file and display results on screen rnagate inputfilename.txt outputfilename.txt -sf command line for subsequence free probability calculation rnagate inputfilename.txt outputfilename.txt -r Note that the input file format is different for -r option. See below.
In order to compile the code, please use Eclipse C++ development tools
You need to install gcc 4.5.0+ to compile and run the code
I used gcc 4.6.0 release verison to compile the code.
* input file format for OPTION = -s or -f or -sf % % comments % 5'UTR sequence must be the first one % % Please follow exact gaps between paragraphs % All inputs must start from the first column % N (number of RNAs involved including UTR) .....((((....))).... %(monomer structure constraint) AGCAGCGCAGGCTUAGAAUG %(initial sequence, if the initial sequnece is not present, put only a # in this line) NNNNNNNNNNGCTUNNNAUG %(monomer sequence constraint, the constraint bases must match with the initial sequence (if provided) in the above line) @@@@@@@@@@RRRRRRRRRR %(constraint when the RNAs make complexes, R means RBS or any associated base that affects translation) X %(number of mutations sites for the UTR) D %(maximum allowed distance of this monomer) Y %(Y = 1 is the computation attempts to preserve, during mutations, the stems of the RNA structures, if Y = 0, no preservation steps taken) .....((((....))).... (monomer structure constraint for sRNA1) # NNNNNNNNNNNNNNNNNNNN %(monomer sequence constraint) @@@@@@@@@@@@@@@@@@@@ %(constraint when the RNAs make complexes) X %(number of mutations sites for the RNA) D %(maximum allowed distance of this monomer) Y %(Y = 1 is the computation attempts to preserve, during mutations, the stems of the RNA structures, if Y = 0, no preservation steps taken) .....((((....))).... %(monomer structure constraint sRNA2 # NNNNNNNNNNNNNNNNNNNN (monomer sequence constraint) @@@@@@@@@@@@@@@@@@@@ (constraint when the RNAs make complexes) X %(number of mutations sites for the sRNA2) D %(maximum allowed distance of this monomer) Y %(Y = 1 is the computation attempts to preserve, during mutations, the stems of the RNA structures, if Y = 0, no preservation steps taken) AND (name of the predefined logic gate that we would like to achieve, the options are YES,NOT,AND, OR,XOR,NAND,XNOR,NOR) BASIC_REAPEAT_CHECK (or EXTENTED_SEQUENCE_CHECK) %(Please see the documentation of check_valid_sequence) MONTE_CARLO_METHOD (or SIMULATED_ANNEALING_METHOD) %(choose the method of calculation) For calculating RBSfree probability:
command line:
rnagate free_in.txt rfree_out.txt -r the input file format. rfee.txt 2 % kcal/mol, sub-optimal energy gap, comments are allowed in the input file. 4 10 % start and end positions of the subsequence % each line of the input file contains an RNA or RNA-complex % RNA sequence one ACGUGUAGUGAUAGUGAGA % another RNA-complex ACGUGUAGUGAUAGUGAGA+GAUGAUAGUAGAUAGCAGC ACGUGUAGUGAUAGUGAGA+GAUGAUAGUAGAUAGCAGC+CGCGGCGAGAGAG Before running RNAGate, the environmental variable RNAGATEHOME, must be set to the home folder of RNAGate which contains rnagate binary and the "parameters" folder
Path tree:
~/ RNAGate/ parameters/ command:
export RNAGATEHOME=~/RNAGate export PATH=$PATH:$RNAGATEHOME if not set, the default value of RNAGATEHOME will be RNAGATEHOME=~/RNAGate