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The bar_map program

The program bar_map computes a mapping between a series of barrier trees as computed by the barriers program. This of interest in particular in the context of co-transcriptional folding, where the one can compute barrier trees corresponding to different length partial transcripts; or for dynamic landscapes produced e.g. when varying the temperature.

The mapping produced by bar_map can be used in conjunction with treekin to compute folding dynamics on time-varying landscape. In the case of co-transcriptional folding, for example, treekin is used to compute folding dynamics for the length of 1 elongation step, the bar_map mapping is then used to transfer the final population onto the next (longer) landscape and thus to obtain the initial condition for the next treekin computation.

For detailed instructions see the BarMap Manpage, and the BarMap Simulator Manpage.

To simplify using bar_map in conjunction with treekin, the barmap_simulator utility produces shell script containing treekin commands for a complete simulation run.

In case you are using our software for your publications you may want to cite:

Ivo L. Hofacker, Christoph Flamm, Christian Heine, Michael T. Wolfing, Gerik Scheuermann and Peter F. Stadler
BarMap: RNA folding on dynamic energy landscapes
RNA 2010 16: 1308-1316, doi:10.1261/rna.2093310


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The latest stable release is from 2008/09/19 and is provided as a perl script.

Get the perl script(s) Download Perl scripts

bar_map v2008/09/19 (*.pl, PerlScript) [6.3kB]
barmap_simulator v2007/04/26 (*.pl, PerlScript) [8.0kB]

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