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RNALOCMIN(1) User Commands RNALOCMIN(1) 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 speci- fied 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) (de- fault=`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 lin- early) (default=`10') --minh=DOUBLE Print only minima with energy barrier greater than this (de- fault=`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') --noLP 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) -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 fold- ing 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 fold- ing 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 --previ- ous 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) (de- fault=off) --just-read Do not expect input from stdin, just do postprocessing. (de- fault=off) -N, --neighborhood Use the Neighborhood routines to perform gradient descend. Cannot be combined with shift move set (-m S) and pseudoknots (-k). Test op- tion. (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. (de- fault=`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 (de- fault=`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 prop- erly only with RNAsubopt -e list. RNAlocmin 2.1.0 July 2017 RNALOCMIN(1)
NAME | SYNOPSIS | DESCRIPTION
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