ensemble-dg, ensemble-dg-same — compute free energy of an ensemble of species
ensemble-dg [OPTION]... PREFIX1 PREFIX2.br ensemble-dg-same [OPTION]... PREFIX
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, ensemble-dg and ensemble-ext instead of running ensemble-dg directly.
- -x, --exclude=A|B|AA|BB
- exclude the specified species from consideration. May be used more than once, to exclude multiple species.
- -H, --enthalpy=dHa,dHb
- assign dHa and dHb kcal/mol of enthalpy to stacking in single strands of A and B, respectively. Must be used with --entropy.
- -S, --entropy=dSa,dSb
- assign dSa and dSb cal/mol/K of entropy to stacking in single strands of A and B, respectively. Must be used with --enthalpy.
- -o, --output=STRING
- name output files with the prefix STRING.
Markham, N. R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. In Keith, J. M., editor, Bioinformatics, Volume II. Structure, Functions and Applications, number 453 in Methods in Molecular Biology, chapter 1, pages 3-31. Humana Press, Totowa, NJ. ISBN 978-1-60327-428-9.
Other references which may be useful may be found at http://www.unafold.org/Dinamelt/dinamelt-references.php
hybrid(1), hybrid-ss(1), concentration(1), concentration-same(1), hybrid2.pl(1)
Nick Markham <firstname.lastname@example.org> and Michael Zuker <email@example.com>
Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.
UNAFold is available from http://www.unafold.org/Dinamelt/software/obtaining-unafold.php. Commercial use requires a license; see https://ipo.rpi.edu/invention/unafold-version-40.