ITC-plot.pl

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Name

ITC-plot.pl - create an isothermal titration calorimetry plot

Synopsis

ITC-plot.pl [OPTION]... FILE1 FILE2

Description

ITC-plot.pl simulates isothermal titration calorimetry (ITC), in which the concentration of one sequence is held constant while that of the other sequence is slowly increased. An ITC plot shows the enthalpy change at each step divided by the change in concentration as a function of concentration.

hybrid and hybrid-ss, or their equivalents, must be run for the five species before running ITC-plot.pl. This is most easily done with hybrid2.pl.

Options

-n, --NA=RNA|DNA
sets nucleic acid type to RNA or DNA. Default is RNA.
-t, --temperature=temp
sets temperature to temp. Default is 37.
-A, --A0=conc
fixes the total concentration of A present at conc molar.
-B, --B0=conc
fixes the total concentration of B present at conc molar.
-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.
-o, --output=prefix
name output files with prefix.
-r, --reuse
assumes that ITC-plot.pl has already been run and creates a new plot based on existing ITC data.
--hyperbolic
creates hyperbolic plots (enthalpy versus concentration) instead of sigmoidal plots (change in enthalpy divided by change in concentration versus concentration).

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. ITC-plot.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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