NAME
concentration, concentration-same — compute mole fractions for each of an ensemble of species
SYNOPSIS
concentration [OPTION]... PREFIX1 PREFIX2.br concentration-same [OPTION]... PREFIX
DESCRIPTION
concentration computes the mole factions of each species in a two-sequence ensemble. In a two-sequence ensemble there are five species: one heterodimer, two homodimers and two monomers. If the sequences are designated 'A' and 'B', then these five species can be labeled AB, AA, BB, A and B. (A can be further subdivided into Af and Au, representing the folded and unfolded states, and likewise for B.) The input to concentration consists of the outputs of running hybrid or hybrid-ss for each of the five species, specifically the five .dG files. (All five runs must have the same temperature range.) concentration writes PREFIX1-PREFIX2.conc which contains the concentrations of A, Af, B, Bf, AA, BB and AB at each temperature. A summary of the options the programs was invoked with is written to PREFIX1-PREFIX2.conc.run.
concentration-same operates in the same manner on a one-sequence ensemble. A one-sequence ensemble consists only of the AA homodimer and the A monomer.
It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl, ensemble-dg and ensemble-ext instead of running concentration directly.
OPTIONS
- -A, --A0=REAL
- set the total concentration of A present to REAL molar.
- -B, --B0=REAL
- set the total concentration of B present to REAL molar.
- -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.
OBSCURE OPTIONS
- -d, --debug
REFERENCES
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
SEE ALSO
hybrid(1), hybrid-ss(1), hybrid2.pl(1)
AUTHORS
Nick Markham <markham@alum.rpi.edu> and Michael Zuker <zukerm@alum.mit.edu>
COPYRIGHT
Copyright (c) 2006-2021, Rensselaer Polytechnic Institute.
AVAILABILITY
Both commercial and non-commercial use of UNAFold require a license from RPI; see https://ipo.rpi.edu/invention/unafold-version-40.