bar_map.pl - analyse dynamic RNA folding landscapes
bar_map.pl [-T temp] [-4] [-d[0|1|2|3]] [-no[GU|CloseGU|LP]] [-logML] [-P paramfile] 1.bar 2.bar [3.bar [...]]
The program reads a series of bar files e.g for different length fragments in the order of the growing chain or for different temperatures in the order of the heating/cooling schedule, and computes which minima in successive barrier trees are equivalent. The program Outputs the correpondence table of minima to STDOUT.
Each column of the output corresponds to the minima of a bar file
(last bar file is the right most gap-less column). The correspondence
between minima of successive columns are calculated by a gradient
walk. Within a row of the output the symbol -> indicates exact
correspondence between the local minima in the succesive barrier trees
while the symbol ~> indicates approximate correspondence with
maximal similarity (= base pair distance). Approximate similarity
arises if forinstance not all minima are listed in the bar file
because the program barriers was used with the -minh option.
Set the ``dangling end'' energies for bases adjacent to helices in free ends and multi-loops: With -d1 only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case. With -d | -d0 dangling ends are ignored altogether. With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.
Display long help message.
Display man page.
With -noGU do not allow GU pairs. With -noCloseGU do not allow GU pairs at the end of helices. With -noLP disallow pairs that can only occur isolated.
Read energy parameters from paramfile.
Rescale energy parameters to a temperature of temp.
Turn off special stabilizing energies for certain tetra-loops.
Ivo L Hofacker, Peter F Stadler, Christoph Flamm
If in doubt our program is right, nature is at fault. Please send comments and bug reports to xtof@tbi.univie.ac.at.