RNALOCMIN

NAME

RNAlocmin − manual page for RNAlocmin 2.1.0

SYNOPSIS

RNAlocmin [OPTIONS]... [FILES]...

DESCRIPTION

RNAlocmin 2.1.0

Calculate local minima from structures via gradient walks. Example usage:

RNAsubopt −p 10000 < "sequence.txt" > "suboptp.txt" RNAlocmin −s "sequence.txt" [OPTIONS] < "suboptp.txt"

−h, −−help

Print help and exit

−−detailed−help

Print help, including all details and hidden options, and exit

−−full−help

Print help, including hidden options, and exit

−V, −−version

Print version and exit

General options:

−s, −−seq=STRING

Sequence file in FASTA format. If the sequence is the first line of the input file, this is not needed (default=‘seq.txt’)

−p, −−previous=STRING

Previously found LM (output from RNAlocmin or barriers), if specified does not need −−seq option

−m, −−move=STRING

Move set: I ==> insertion & deletion of base pairs S ==> I&D& switch of base pairs (possible values="I", "S" default=‘I’)

−n, −−min−num=INT

Maximal number of local minima returned (0 == unlimited) (default=‘100000’)

−−find−num=INT

Maximal number of local minima found (default = unlimited − crawl through whole input file)

−v, −−verbose−lvl=INT

Level of verbosity (0 = nothing, 4 = full) WARNING: higher verbose levels increase the computation time (default=‘0’)

−−depth=INT

Depth of findpath search (higher value increases running time linearly) (default=‘10’)

−−minh=DOUBLE

Print only minima with energy barrier greater than this (default=‘0.0’)

−−minh−lite

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)

−w, −−walk=STRING

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’)

−e, −−useEOS

Use energy_of_structure_pt calculation instead of energy_of_move (slower, it should not affect results) (default=off)

−P, −−paramFile=STRING

Read energy parameters from paramfile, instead of using the default parameter set

−d, −−dangles=INT

How to treat "dangling end" energies for bases adjacent to helices in free ends and multi−loops

(default=‘2’)

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−barriers=STRING

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

−k, −−pseudoknots

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)

−−just−read

Do not expect input from stdin, just do postprocessing. (default=off)

−N, −−neighborhood

Use the Neighborhood routines to perform gradient descend. Cannot be combined with shift move set (−m S) and pseudoknots (−k). Test option. (default=off)

−−degeneracy−off

Do not deal with degeneracy, select the lexicographically first from the same energy neighbors. (default=off)

−−just−output

Do not store the minima and optimize, just compute directly minima and output them. Output file can contain duplicates. (default=off)

Barrier tree:

−b, −−bartree

Generate an approximate barrier tree. (default=off)

−−barr−name=STRING

Name of barrier tree output file, switches on −b flag. (default=‘treeRNAloc.ps’)

Kinetics (rates for treekin program):

−−barrier−file=STRING

File for saddle heights between LM (simulates the output format of barriers program)

−r, −−rates

Create rates for treekin (default=off)

−f, −−rates−file=STRING

File where to write rates, switches on −r flag (default=‘rates.out’)

−T, −−temp=DOUBLE

Temperature in Celsius (only for rates) (default=‘37.0’)

Flooding parameters (flooding occurs only with -r, -b, or --minh option):

−−floodPortion=DOUBLE

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’)

−−floodMax=INT

Flood cap − how many structures to flood in one basin (default=‘1000’)

Miscelaneous:

−−numIntervals=INT

Number of intervals for Jing’s visualisation (default=‘0’)

−−eRange=FLOAT

Report only LM, which energy is in range <MFE (or lowest found LM), MFE+eRange> in kcal/mol.

−−allegiance=STRING

Filename where to output the allegiance of structures. Works properly only with RNAsubopt −e list.