The DINAMelt Server
Prediction of Melting Profiles for Nucleic Acids
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Table of Contents
ITC-plot.pl - create an isothermal titration calorimetry plot
ITC-plot.pl [OPTION]... FILE1 FILE2
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.
- -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).
- 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).
hybrid(1), hybrid-ss(1), hybrid2.pl(1)
 |
Nicholas R. Markham
Department of Computer Science |
Michael Zuker
Department of Mathematical Sciences |
Rensselaer Polytechnic Institute
2005-01-18 |