bar_map.pl − analyse dynamic RNA folding landscapes
[−T temp] [−4] [−d[0|1|2|3]]
[−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 firstname.lastname@example.org.