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Prediction of Melting Profiles for Nucleic Acids

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Name

concentration, concentration-same - compute mole fractions for each of an ensemble of species

Synopsis

concentration [OPTION]... PREFIX1 PREFIX2
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 heterodimer and the A monomer.

It is recommended to use hybrid2.pl to run hybrid, hybrid-ss, concentration, concentrations.pl and ensemble-dg and ensemble-ext instead of running concentration directly.

Options

-A, --A0=conc
specifies the total concentration of A present to conc molar.
-B, --B0=conc
specifies the total concentration of B present to conc molar.
-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. Different values for the two sequences may be specified delimited by a comma. 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. Different values for the two sequences may be specified delimited by a comma. 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.

See Also

hybrid(1), hybrid-ss(1), hybrid2.pl(1)

Table of Contents

RPI logo Nicholas R. Markham
Department of Computer Science		 Michael Zuker
Department of Mathematical Sciences
Rensselaer Polytechnic Institute
2005-01-18