Tree-decomposition based dynamic programming algorithm for multiple target RNA design
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RNARedPrint.pro

README.md

RNARedPrint

Tree-decomposition based dynamic programming algorithm for multiple target RNA design

Prerequisites

  • g++ 5.1.1+
  • java7 compiler and runtime environment

Usage

This first prototype only computes the number of sequences compatible with a set of secondary structures.

To count the number of sequences compatible with a bunch of secondary structures

  • ((((....))))
  • ((((..))))..
  • ..((((..))))

first clone the project, move into the directory:

  • cd bin
  • make -C ..
  • RNARedPrint "((((....))))" "((((..)))).." "..((((..))))"