RiboLogic

RiboLogic is a Python package for designing RNAs to adopt specified secondary structures in multiple conditions.

See example_run.sh for example usage. Be sure to change YOUR_CODE_DIR to the path to your code.

Dependencies

Python

Python2.7+, Python packages: numpy, matplotlib, requests, networkx.

NUPACK

Add the following to your bashrc

export NUPACKHOME=/path/to/RiboLogic/resources/nupack

Input file format

Input files contain the following types of entries.

Inputs

Inputs, including ligands and RNAs, are specified using the input symbol <. For RNA inputs, specify the sequence on the subsequent line.

<myRNA
AUGCAUGC

For ligand inputs, specify the Kd of the ligand (in the same units as concentration is specified subsequently) and the secondary structure constraints of the aptamer

<myligand
1.5e-6
......................(((xxxxxx(((........................)))xxxxx))).....

Sequence constraints

Sequence constraints are specified using the input symbol -. Characters must be A, U, G, C or N.

-sequence
NNNNNNNNNNAUGCNNNNNNNNNNN

Fixed subsequences that can be located anywhere in the full sequence can be specified as follows.

-variable
AAAA

For each variable element, you must add two additional lines to the secondary structure constraints specifying any constraints on the variable element.

In addition, you can specify subsequences that should not occur using x.

xGGGG

Secondary structure constraints

Secondary structure constraints, indicated by >, may be specified for various conditions. They can have one of the following types: single (no inputs), oligos (RNA inputs), and aptamer (ligand inputs). The constraints are specified by one line with the desired secondary structure and a second line that specifies the bases that should be constrained (x = constrained, o = unconstrained, p = paired (to any other base), n = anything that is not what is given)

>single
.....(((((.........))))).
oooooxxxxxxxxxxxxxxxxxxxo

For oligos type, the second line should specify the RNAs and their concentrations (in M).

>oligos
myRNA 200e-6; myRNA2 100e-6
.....(((((.......))))))).
ooooooonnnooooooonnnnnooo

For aptamer type, the second line should specify the ligand and its concentration.

>aptamer
myligand 200e-6
.....(((((.......))))))).
ooooooonnnooooooonnnnnooo

For bases that need to be paired but not to a specific base, use |. You can supply an optional threshold parameter on the line following the constraints. In the following example, the design must have at least 5 paired bases in the indicated region.

>single
.....||||||||............
oooooppppppppoooooooooooo
5