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