UNAFold.pl

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Name

UNAFold.pl - fold an RNA or DNA sequence with lots of output

Synopsis

UNAFold.pl [OPTION]... FILE [FILE]

Description

If one FILE is specified, UNAFold.pl folds the (first) sequence in FILE with hybrid-ss-min, and then computes the h-num and ss-count values. If two FILEs are specified, UNAFold.pl hybridized the first sequence in each FILE with hybrid-min. All output files are named with a prefix which consists of the file name(s) with the extension .seq removed. The loop free energy decomposition is written to prefix.det or prefix.det.html. If boxplot_ng is available, the enrgy dot plot is created in Postscript format and, if possible, in PNG, JPEG or GIF format. Likewise, if sir_graph_ng or sir_graph is available, each structure is drawn in Postscript and, if possible, PNG/JPEG/GIF formats. In addition, each structure is available in XRNA ss format, and the complete set of foldings in RNAML format is written to prefix.rnaml. Finally, in HTML mode, prefix.html contains links to all of the output.

Options

-n, --NA=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-t, --temp=temperature
sets folding temperature to temperature. 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).
-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.)
-m, --maxbp=value
Bases farther apart than value cannot form. Default is no limit.
-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.
-C, --circular
treats sequences as circular rather than linear.
-P, --percent=value
sets the energy increment to value percent. Defauls is 5.
-W, --window=value
sets the window parameter to value. Default is determined by sequence length.
-X, --max=value
sets the maximum number of foldings to value. Default is 100.
--ann=none|p-num|ss-count
optionally produces plots annotated with p-num or ss-count values. Default is none.
--mode=auto|bases|lines
produces structures drawn with bases or lines. Default is auto.
--label=number
labels every numberth base.
--rotate=angle
rotates structures by angle degrees.
--run-type=text|html
produces output in plain text (the default) or HTML.
--model=EM|PF
performs an energy minimization (the default) or partition function calculation. In partition function mode, stochastic tracebacks replace the mfold sample and a probability dot plot replaces the energy dot plot.

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.)

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. UNAFold.pl 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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