RNAfbinv 2.0

RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.
The similarity is based on fragment based design. A tree alignment is done based on nodes (structural motifs).
Nodes are comparable if they are both bounded motifs (stems) or unbounded motifs (multi loop, interior loops, bulges ect...).
Each iteration the target motif tree will be aligned to the current candidate tree.
The best alignment with the addition of other valuable features will generate a design score.
Design score of 0 is exact fit but even higher scores can generate a good candidate.

Attaching Vienna RNA

Vienna RNA package is required for RNAfbinv to work. This must be installed separately.
Current version was tested with Vienna 2.4 and above. RNAfbinv will identify Vienna package if it's bin directory is in PATH.
If you wish to link a specific installation of Vienna set the VIENNA_PATH environment variable to the correct bin directory.

You can set Vienna location in python

import os
os.environ['VIENNA_PATH'] = "VIENNA_BIN_DIR_PATH"

or directly via the vienna script

from rnafbinv import vienna
vienna.set_vienna_path("VIENNA_BIN_DIR_PATH")

Usage

The design process can be ran using the following code:

from rnafbinv import RNAfbinvCL
RNAfbinvCL.main(command_line_arguments)

To generate a tree for a specific sequence / structure:
Structure is a dot bracket notation structure and sequence is an IUPAC string with the same length

from rnafbinv import shapiro_tree_aligner
shapiro_tree_aligner.get_tree(sructure, sequence)

To compare two trees and score them: alignment_rules has a default value and is optional

from rnafbinv import shapiro_tree_aligner
shapiro_tree_aligner.align_trees(source_tree, tree_target, alignment_rules)

Command line arguments:

Usage: python3 RNAsfbinvCL [Options]
    -h : Shows usage text
    -i <number of iterations> : sets the number of simulated annealing iterations (default is 100)
    --seed <random number generator seed> : a long number that is used by the random number generator
    -t <number of look ahead attempts> : number of look head mutation attempts for each iteration (default is 4)
    -e : designs a circular RNA (default is False)
    -m <motif[,...]> : comma separated list of motifs to preserve
                       motif: <motif No>[M|H|E|I|S|B]<motif No of bases>
                       Use ListMotifs.listMotif(structure) to retrieve a list of legal motifs for a given structure,  
    -s <starting sequence> : the initial sequence for the simulated annealing process
    -r : force starting simulated annealing with a random sequence
    -p <MFE|centroid> : uses RNAfold centroid or MFE folding. (default is MFE)
    --verbose : Additional info message on simulation process
    --debug : Debug information
    -l <log file path> : Logging information will be written to a given file path (rewrites file if exists)
    --length <length diff> : The resulting sequence size is target structure length +- length diff (default it 0)

    -f <input file path> : Path of ini file that includes mandatory information. Some options can also be set via file.
                           command line options take precedence.
    List of available configurations (* are mandetory and will be requested via command line if not inserted):
    *TARGET_STRUCTURE=<target structure>
    *TARGET_SEQUENCE=<target sequence>
    TARGET_ENERGY=<target energy>
    TARGET_MR=<target mutational robustness>
    SEED=<random seed>
    STARTING_SEQUENCE=<starting sequence>
    ITERATION=<number of simulated annealing iterations>

File input:

# mandatory
TARGET_STRUCTURE=<target structure>
TARGET_SEQUENCE=<target sequence>
# optional
TARGET_ENERGY=<target energy>
TARGET_MR=<target mutational robustness>
SEED=<random seed>
STARTING_SEQUENCE=<starting sequence>
ITERATION=<number of simulated annealing iterations>

GUI / Command line

You can download the RNAfbinv wrapper from RNAfbinv2.0 user application
It includes python code to run the GUI / command line and the VARNA java package to generate 2D images.
If you remove the VARNA jar or do not have java installed, images will not be generated but the design process will proceed normally.

To run command line just use the '-cl' flag for RNAfbinv.py. by default a GUI version will run.

To specify Vienna package location please update the 'VIENNA' parameter in config.ini (or set VIENNA_PATH environment variable)
To specify Java location please update the 'JAVA' parameter in config.ini (or set JAVA_PATH environment variable)
In both cases you need to specify the folder where the binary file sits. Only needed if not specified in PATH.

Webserver

RNAfbinv2.0 can be found in a web server combined with incaRNAtion. The webserver generates starting seeds using incaRNAtion global sampling algorithm.
Te seed sequences are then sent to RNAfbinv2.0 for design. incaRNAfbinv web server