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Julia interface to dss-opt RNA sequence design programs

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DssOpt.jl

Julia interface to dss-opt RNA sequence design programs.

Installation

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

Usage

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

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Julia interface to dss-opt RNA sequence design programs

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