https://github.com/marcom/dss-opt

Dynamics in sequence space optimisation for RNA sequence design
https://github.com/marcom/dss-opt

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Dynamics in sequence space optimisation for RNA sequence design

• Host: GitHub
• URL: https://github.com/marcom/dss-opt
• Owner: marcom
• License: gpl-3.0
• Created: 2012-07-06T15:48:45.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2023-08-01T11:28:31.000Z (over 1 year ago)
• Last Synced: 2024-11-13T03:07:49.611Z (2 months ago)
• Language: C
• Size: 195 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: COPYING

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README

        
# dss-opt: Dynamics in Sequence Space Optimisation

RNA sequence design for a given target secondary structure.  Sequences

are designed by optimising a design score in a continuous sequence

space, allowing a mixture of bases at each position during

optimisation.

## Citation

Marco C. Matthies, Stefan Bienert, Andrew E. Torda. Dynamics in

Sequence Space for RNA Secondary Structure Design. J. Chem. Theory

Comput., 2012, 8, 10, 3663--3670.

https://doi.org/10.1021/ct300267j

## Running the program

The dynamics in sequence space optimisation is performed with the program `opt-md`.

The `opt-sd` and `opt-sd-gsl` programs perform sequence design by gradient descent alone

and are not described in the paper.

```

# show command-line arguments

./opt-md -h

# design a sequence for the target structure ((((...))))

./opt-md '((((...))))'

# you can often improve the quality of designed sequences by playing with

# the --kneg and --khet parameters, which change the weights of the negative

# design and sequence heterogeneity terms, as well as other parameters

```

## Build instructions

The code can be compiled by running `make` in this directory. You need

the GSL (GNU Scientific Library) header files and library installed

(`libgsl-dev` package in Ubuntu).

Additionally, there is a little utility program called

`rna-ensemble-distance` that uses the ViennaRNA library to compute the

target probability and ensemble defect of a designed sequence with

respect to a given target structure.  You can find it in the

`rna-ensemble-distance-with-ViennaRNA/` directory. The README file in

the

[rna-ensemble-distance-with-ViennaRNA/](./rna-ensemble-distance-with-ViennaRNA/)

directory contains instructions on how to build this utility.

## Python interface

The beginnings of a python interface can be found in the directory

`python/`.  Install it with

```sh

pip install python/

# alternatively, if you want to run the python unit tests, do

pip install python/[test]

# run the python unit tests

pytest

```

Example usage:

```python

import dssopt

dssopt.opt_md('(((...)))')

```

## Energy parameters

The parameters for the RNA nearest neighbour energy model were

converted from ViennaRNA, many thanks to them.  The parameters were

converted from the ViennaRNA-1.8.5 `param/vienna17.par` parameter file

to C code with `scripts/vienna_parse_param.py`. The generated C code

containing the parameters can be found in `nn_param.c`.

## Copyright and license

All code was written by Marco Matthies, Centre for Bioinformatics,

Hamburg and is licensed under the GNU General Public License, version

3 or later.