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')

       --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 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.