hybrid-ss-min

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Name

hybrid-ss-min - fold an RNA or DNA sequence

Synopsis

hybrid-ss-min [OPTION]... FILE

Description

hybrid-ss-min computes a minimum energy folding of the sequence(s) in FILE. If the suffix option is used, the folding is computed using the energy rules with the suffix extension; otherwise, it is computed at each temperature from tMin to tMax degrees Celsius, in increments of tInc degrees. All output files are named with a prefix which consists of the file name with the extension .seq removed. The free energy at each temperature is written to prefix.dG. The minimum energy structure is written to prefix.temperature.ct. hybrid-ss-min also writes prefix.temperature.plot and prefix.temperature.ext in the manner of hybrid-ss; each probability is either 1 or 0. A summary of the options the program was invoked with is written to prefix.run.

Options

-n, --NA=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-t, --tmin=temp
sets minimum temperature to temp. Default is 37.
-i, --tinc=temp
sets temperature increment to temp. Default is 1.
-T, --tmax=temp
sets maximum temperature to temp. Default is 37.
-N, --sodium=value
sets Sodium ion concentration to value molar. Default is 1.
-M, --magnesium=value
sets Magnesium ion concentration to value molar. Default is 0.
-p, --polymer
use salt corrections for polymers instead of oligomers (the default).
-s, --suffix=string
use energy rules with the suffix string. Overrides --tmin, --tinc, --tmax, --sodium, --magnesium and --polymer.
-o, --output=prefix
name output files with prefix.
-r, --prohibit=i,j[,k]
prohibit all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, prohibit bases i to i+k-1 from pairing at all; if i is 0, prohibit bases j to j-k+1 from pairing at all. k defaults to 1 if not specified.
-f, --force=i,j[,k]
force all basepairs in the helix from i,j to i+k-1,j-k+1. If j is 0, forces bases i to i+k-1 to be double-stranded; if i is 0, forces bases j to j-k+1 to be double-stranded. k defaults to 1 if not specified.
-E, --energyOnly
skips computation of structure and outputs only prefix.dG and prefix.run. This mode uses less time and memory.
-I, --noisolate
prohibits all isolated basepairs. Isolated basepairs are helices of length 1; that is, they do not stack on another basepair on either side. (See also the --prefilter option below.)
-F, --mfold=P,W,MAX
causes hybrid-ss-min to perform multiple (suboptimal) tracebacks in the style of mfold. P indicates the percent suboptimality to consider; only structures with energies within P% of the minimum will be output. W indicates the window size; a structure must have at least W basepairs that are each a distance of at least W away from any basepair in a previous structure. MAX represents an absolute limit on the number of structures computed. When --mfold is specified, hybrid-ss-min also writes prefix.ann and prefix.plot. These files contain the p-num values and the energy dot plot, respectively.
-m, --maxbp=value
Bases farther apart than value cannot form. Default is no limit.
-q, --quiet
In quiet mode hybrid-ss-min interprets the arguments on the command line as sequences themselves, rather than as names of files containing sequences. In addition, no files are written and standard output consists only of the free energies.
-c, --constraints=file
reads a list of constraints from file. Constraints must be in the form "P i j k" or "F i j k". These are equivalent to specifying "--prohibit=i,j,k" and "--force=i,j,k", respectively. If file is not specified, it defaults to prefix.aux.
-b, --basepairs=file
reads a list of allowable helices from file. Each helix consists of three whitespace-delimited numbers which specify the starting basepair and the length of the helix. When this option is used, all basepairs except those in file are prohibited from forming.
-C, --circular
treats sequences as circular rather than linear.

Obscure Options

--allpairs
allows basepairs to form between any two nucleotides. When --allpairs is not specified, only Watson-Crick and wobble basepairs are allowed.
--maxloop=size
sets the maximum size of bulge/interior loops to size. Default is 30.
--nodangle
removes single-base stacking from consideration.
--simple
makes the penalty for multibranch loops constant rather than affine.
--prefilter=value1[,value2]
Sets the prefilter to filter out all basepairs except those in groups of value2 adjacent basepairs of which value1 can form. value2 is the same as value1 if unspecified. Default is 2 of 2. (See also the --noisolate option above.)
--stream
reads sequences from standard input rather than a file. Quiet mode is implied, so that free energies are written on standard output and no files are created.

Environment

UNAFOLDDAT
an alternate location from which to read the energy rules. The default energy rules can be overridden with files in the current directory or in the directory pointed to by UNAFOLDDAT. hybrid-ss-min looks for each file first in the current directory, then in the directory specified by UNAFOLDDAT and last in /usr/local/share/unafold (or wherever the energy rules were installed).

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