hybrid-ss-2s.pl

Table of Contents

Name

hybrid-ss-2s.pl - fold an RNA or DNA sequence

Synopsis

hybrid-ss-2s.pl [OPTION]... FILE

Description

hybrid-ss-2s.pl computes a minimum energy folding of the sequence(s) in FILE using hybrid-ss-min and evaulates its enthalpy and entropy. It then calculates the free energy at each temperature in a range and writes a .dG file. hybrid-ss-2s.pl also makes a copy of the .ext file for each temperature, so that it can act as a replacement for hybrid-ss, for example in hybrid2.pl.

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).
-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.
-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.)
-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.
--temperature=temp
sets the temperature at which the minimum-energy folding is computed. Default is 37.

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. hybrid-ss-2s.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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