hybrid-ss / hybrid-ss-simple / hybrid-ss-noml

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Name

hybrid-ss, hybrid-ss-simple, hybrid-ss-noml - fold an RNA or DNA sequence

Synopsis

hybrid-ss [OPTION]... FILE
hybrid-ss-simple [OPTION]... FILE
hybrid-ss-noml [OPTION]... FILE

Description

hybrid-ss computes a partition function for the folding of the sequence 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 partition function and associated free energy at each temperature are written to prefix.dG. The probabilities of each possible base pair occurring are written to prefix.temperature.plot and the probabilities of each base and each pair of adjacent bases being single-stranded are written to prefix.temperature.ext. A summary of the options the program was invoked with is written to prefix.run.

hybrid-ss-simple is identical in function to hybrid-ss when the --nodangle and --simple options are used, but hybrid-ss-simple is faster and uses less memory.

hybrid-ss-noml is identical in function to hybrid-ss except that multibranch loops are not allowed. Like hybrid-ss-simple, it is faster and uses less memory than hybrid-ss.

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 0.
-i, --tinc=temp
sets temperature increment to temp. Default is 1.
-T, --tmax=temp
sets maximum temperature to temp. Default is 100.
-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 probabilities 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 and --nopostfilter options below.)
-z, --zip
enforces "zipping up" helices by forcing single-stranded bases to dangle on adjacent basepairs when possible.
-k, --tracebacks=number
computes number stochastic tracebacks and writes them to prefix.temperature.ct. Stochastic tracebacks are computed according to the Boltzmann probability distribution so that the probability of a structure is its Boltzmann factor divided by the partition function.
-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.
-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.

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.)
--nopostfilter
Disables the postfilter. The postfilter, which is enabled by default, removes from consideration all structures that consist of only one basepair.

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 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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