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:
BarMap: RNA folding on dynamic energy landscapes
RNA 2010 16: 1308-1316, doi:10.1261/rna.2093310
News
-
No recent news.
Download
Download Perl scripts
bar_map v2008/09/19
(*.pl, PerlScript) [6.3kB]
barmap_simulator v2007/04/26
(*.pl, PerlScript) [8.0kB]
Comments and Bug Reports
If in doubt our program is right, nature is at fault.
Comments and bug reports should be sent to rna@tbi.univie.ac.at