RNAcop is available as standalone command-line tool (implemented in C in the ViennaRNA package framework). Furthermore, we provide utility scripts for data processsing and visualization, as well as the heuristic findgoodregion for selecting flanking regions. The RNAcop frame work can be downloaded as a bundle including utility scripts and findgoodregion.

RNAcop bundle:

RNAcop-1.03-bundle.tar.gzRNAcop frame work (using ViennaRNA 2.1.9)
RNAcop-1.02-bundle.tar.gzRNAcop frame work

RNAcop version history:

RNAcop-1.03.tar.gzchanged to ViennaRNA 2.1.9
RNAcop-1.02.tar.gzuses ViennaRNA 2.1.1; changes in command-line options
RNAcop-1.01.tar.gza version only for test purposes excluding dangling end energy contributions; contains some minor changes
RNAcop-1.0.tar.gzinitial functional version

RNAcop utility:

utility.tar.gzutility scripts for data processing and visualiziation

RNAcop findgoodregion (heuristic for selecting flanking regions):

findgoodregion-0.2.tar.gzfixed output if only optimal solution present;changed default parameters
findgoodregion-0.1.tar.gzinitial release

For comments, suggestions for improvement or bug reports contact Nikolai Hecker: hecker(at)rth.dk