https://github.com/marcom/dssopt.jl

Julia interface to dss-opt RNA sequence design programs
https://github.com/marcom/dssopt.jl

Last synced: 8 days ago
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Julia interface to dss-opt RNA sequence design programs

• Host: GitHub
• URL: https://github.com/marcom/dssopt.jl
• Owner: marcom
• License: other
• Created: 2022-09-23T15:43:03.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-11-05T20:39:51.000Z (about 1 year ago)
• Last Synced: 2024-11-13T03:07:49.408Z (2 months ago)
• Language: Julia
• Size: 67.4 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# DssOpt.jl

Julia interface to [dss-opt](https://github.com/marcom/dss-opt) RNA

sequence design programs.

## Installation

```julia

using Pkg

pkg"add https://github.com/marcom/DssOpt_jll.jl"

pkg"add https://github.com/marcom/DssOpt.jl"

```

## Usage

```julia

using DssOpt

# dynamics in sequence space optimisation with dynamical simulated

# annealing

opt_md("(((...)))")

opt_md("(((...)))"; verbose=true)

# steepest descent optimisiation

opt_sd("(((...)))")

opt_sd_gsl("(((...)))")

```

## References

Matthies, Bienert, Torda. Dynamics in sequence space for RNA secondary

structure design, JCTC, 3663 -- 3670, 2012.

https://doi.org/10.1021/ct300267j