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ensemble-dg / ensemble-dg-same
Name
ensemble-dg, ensemble-dg-same - compute free energy of an ensemble of species
Synopsis
ensemble-dg [OPTION]... PREFIX1 PREFIX2
ensemble-dg-same [OPTION]... PREFIX
Description
ensemble-dg computes the free energy fo a two-sequence ensemble. The input to ensemble-dg consists of the outputs of running hybrid or hybrid-ss on each species, as well as the output of running concentration on the ensemble. ensemble-dg writes PREFIX1-PREFIX2.ens.dG which containts the partition function and free energy of the ensemble at each temperature.
ensemble-dg-same operates in the same manner on a one-sequence ensemble, using the output from concentration-same.
It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl and ensemble-dg and ensemble-ext instead of running ensemble-dg directly.
Options
- -x, --exclude=A|B|AA|BB
- excludes the specified species from consideration. May be used more than once, to exclude multiple species.
- -H, --enthalpy=value
- assigns value kcal/mol of enthalpy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --entropy.
- -S, --entropy=value
- assigns value cal/mol/K of entropy to stacking in single strands, in proportion to the lengths of the sequences. Must be used with --enthalpy.
- -o, --output=prefix
- names output files with prefix.
- -Y, --infinity
- enables "infinite temperature correction": the partition functions for each species are corrected according to values in A.inf, B.inf, A-A.inf, B-B.inf and A-B.inf.
Table of Contents
UNAFold Man pages
- concentration / concentration-same
- concentrations.pl / concentrations-same.pl
- ct2rnaml
- ct-energy
- ct-energy-det.pl
- ct-ext
- ct-prob
- ct-uniq
- dG2Cp
- dG2dH / dG2dS
- ensemble-dg / ensemble-dg-same
- ensemble-ext / ensemble-ext-same
- h-num.pl
- hybrid
- hybrid2.pl
- hybrid-2s.pl
- hybrid-min
- hybrid-plot / hybrid-plot-ng
- hybrid-select.pl
- hybrid-ss / hybrid-ss-simple / hybrid-ss-noml
- hybrid-ss-2s.pl
- hybrid-ss-min
- ITC-plot.pl
- melt.pl
- plot2ann.pl
- ss-count.pl
- UNAFold.pl
- vantHoff-plot.pl