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=RNA2|RNA|DNA
- set nucleic acid type to RNA or DNA. Default is RNA.
- -t, --temperature=REAL
- set temperature to REAL °C. Default is 37.
- -A, --A0=REAL
- fix the total concentration of A present at REAL molar.
- -B, --B0=REAL
- fix the total concentration of B present at REAL molar.
- -x, --exclude=A|B|AA|BB
- exclude the specified species from consideration. May be used more than once, to exclude multiple species.
- --fraction=REAL
- assign the fraction REAL 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
- remove stacking in unfolded single strands from consideration.
- --Tmelt=REAL
- assign entropy to single strands so that melting temperature is REAL °C. Default is 50.
- -o, --output=prefix
- name output files with prefix.
- -r, --reuse
- assume that ITC-plot.pl has already been run and create a new plot based on existing ITC data.
- --hyperbolic
- create 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).
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.