RNAlocmin − manual page for RNAlocmin 2.1.0
RNAlocmin [OPTIONS]... [FILES]...
Calculate local minima from structures via gradient walks. Example usage:
RNAsubopt −p 10000 < "sequence.txt" > "suboptp.txt" RNAlocmin −s "sequence.txt" [OPTIONS] < "suboptp.txt"
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Sequence file in FASTA format. If the sequence is the first line of the input file, this is not needed (default=‘seq.txt’)
Previously found LM (output from RNAlocmin or barriers), if specified does not need −−seq option
Move set: I ==> insertion & deletion of base pairs S ==> I&D& switch of base pairs (possible values="I", "S" default=‘I’)
Maximal number of local minima returned (0 == unlimited) (default=‘100000’)
Maximal number of local minima found (default = unlimited − crawl through whole input file)
Level of verbosity (0 = nothing, 4 = full) WARNING: higher verbose levels increase the computation time (default=‘0’)
Depth of findpath search (higher value increases running time linearly) (default=‘10’)
Print only minima with energy barrier greater than this (default=‘0.0’)
When flooding with −−minh option, search for only saddle (do not search for a LM that is lower). Increases efficiency a tiny bit, but when turned on, the results may omit some non−shallow minima, especially with higher −−minh value. (default=off)
Walking method used D ==> gradient descent F ==> use first found lower energy structure R ==> use random lower energy structure (does not work with −−noLP and −m S options) (possible values="D", "F", "R" default=‘D’)
Work only with canonical RNA structures (w/o isolated base pairs, cannot be combined with ranodm walk (−w R option) and shift move set (−m S)) (default=off)
Use energy_of_structure_pt calculation instead of energy_of_move (slower, it should not affect results) (default=off)
Read energy parameters from paramfile, instead of using the default parameter set
How to treat "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, this is the default for mfe folding but unsupported for the partition function folding.
With −d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for partition function folding (−p). The option −d0 ignores dangling ends altogether (mostly for debugging). 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.
Note that by default (as well as with −d1 and −d3) pf and mfe folding treat dangling ends differently. Use −d2 in addition to −p to ensure that both algorithms use the same energy model.
Fix barrier file for interior loops (just recompute if all LM in barrier output are LM), if specified, does not need neither −−previous nor −−seq option
Allow for pseudoknots according to "gfold" model − H, K, L, and M types (genus one) of pseudoknots are allowed (increases computation time greatly), cannot be combined with shift move set (−m S) (default=off)
Do not expect input from stdin, just do postprocessing. (default=off)
Use the Neighborhood routines to perform gradient descend. Cannot be combined with shift move set (−m S) and pseudoknots (−k). Test option. (default=off)
Do not deal with degeneracy, select the lexicographically first from the same energy neighbors. (default=off)
Do not store the minima and optimize, just compute directly minima and output them. Output file can contain duplicates. (default=off)
Generate an approximate barrier tree. (default=off)
Name of barrier tree output file, switches on −b flag. (default=‘treeRNAloc.ps’)
(rates for treekin program):
File for saddle heights between LM (simulates the output format of barriers program)
Create rates for treekin (default=off)
File where to write rates, switches on −r flag (default=‘rates.out’)
Temperature in Celsius (only for rates) (default=‘37.0’)
parameters (flooding occurs only with -r, -b, or --minh
Fraction of minima to flood (floods first minima with low number of inwalking sample structures) (0.0 −> no flood; 1.0 −> try to flood all) Usable only with −r or −b options. (default=‘0.95’)
Flood cap − how many structures to flood in one basin (default=‘1000’)
Number of intervals for Jing’s visualisation (default=‘0’)
Report only LM, which energy is in range <MFE (or lowest found LM), MFE+eRange> in kcal/mol.
Filename where to output the allegiance of structures. Works properly only with RNAsubopt −e list.