hybrid2.pl

Table of Contents

Name

hybrid2.pl - simulate a one- or two-sequence ensemble of nucleic acids

Synopsis

hybrid2.pl --A0=A0 --B0=B0 [OPTION]... FILE1 FILE2

Description

hybrid2.pl simulates an ensemble of two RNA or DNA sequences. Such an ensemble consists of five species - one heterodimer, two homodimers and two monomers - but species known to be irrelevant can be excluded to save time. In its default mode, hybrid2.pl operates by running hybrid to simulate each dimer and hybrid-ss to simulate each monomer. It then runs concentration and concentrations.pl to compute mole fractions of each species, followed by ensemble-dg and ensemble-ext to compute the free energy and UV absorption of the ensemble. Finally, hybrid2.pl runs dG2dH, dG2dS and dG2Cp on the ensemble free energy.

In addition to the output of each subprogram it runs, hybrid2.pl produces extra output in the form of Postscript plots produced wth gnuplot. The plots are named with a prefix consisting of the prefixes of each file concatenated with a hyphen. The fraction of each species present is plotted versus temperature in prefix.conc.ps, the ensemble heat capacity (with melting temperature indicated) in prefix.Cp.ps and the ensemble extinction in prefix.ext.ps. In each case, the file of gnuplot commands is also saved with an extension of .gp.

If FILE2 is not specified or is the same as FILE1, or if the two files contain the same sequence, hybrid2.pl simulates a one-sequence ensemble instead. In this case, there are two species (monomer and homodimer) and hybrid2.pl runs concentration-same, concentrations-same.pl, ensemble-dg-same and ensemble-ext-same in place of their two-sequence counterparts.

Under certain circumstances hybrid2.pl may substitute other programs for hybrid and hybrid-ss. If the --nodangle and --simple options are given, hybrid-ss-simple replaces hybrid-ss, because this saves time while giving the same results. If hybrid2.pl is invoked as hybrid2-min.pl, hybrid-min and hybrid-ss-min replace hybrid and hybrid-ss-min, so that the entire computation is performed using energy minimization rather than partition function calculations. Likewise, if hybrid2.pl is invoked as hybrid2-2s.pl, hybrid-min-2s.pl and hybrid-ss-2s.pl replace hybrid and hybrid-ss, so that a generalized two-state computation is performed. Finally, if hybrid2.pl is invoked with "-x" in the name (hybrid2-x.pl, hybrid2-min-x.pl or hybrid2-2s-x.pl) all species except the heterodimer are excluded. Thus hybrid2-2s-x.pl performs a "traditional" two-state calculation.

Options

Most of the options below are passed to the subprograms to which they apply, but some (--fraction, --Tmelt, --parallel and --reuse) affect the behavior of hybrid2.pl directly.

-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).
-A, --A0=conc
sets the total concentration of A present to conc molar.
-B, --B0=conc
sets the total concentration of B present to conc molar.
-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.
-m, --maxbp=value
Bases farther apart than value cannot form. Default is no limit.
-x, --exclude=A|B|AA|BB
excludes the specified species from consideration. May be used more than once, to exclude multiple species.
--fraction=value
assigns value of the stacking enthalpy for each sequence with its reverse complement to stacking in the single strands. Default is 0.1. To disable entirely, use --nofraction.
--nofraction
removes stacking in unfolded single strands from consideration.
--Tmelt=temp
assigns entropy to single strands so that melting temperature is temp. Default is 50.
-P, --parallel
runs the calculations for each species at the same time, rather than sequentially. This option results in a significant speedup on multiprocessor machines.
-r, --reuse
assumes that hybrid and hybrid-ss have already been run, and only runs the ensemble computations.
--title=string
uses string as the title for plots.

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.
--single
only sum extinctions for each nucelotide, rather than for each dinucleotide.
--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. hybrid2.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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