vantHoff-plot.pl

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Name

vantHoff-plot.pl - create a van't Hoff plot.

Synopsis

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

Description

vantHoff-plot.pl creates a van't Hoff plot, in which the inverse of melting temperature is plotted as a function of the logarithm of total strand concentration. For a two-state melt, this results in a line with slope equal to R divided by the enthalpy change.

hybrid and hybrid-ss, or their equivalents, must be run for the five species before running vantHoff-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.
-C, --Ct=conc
sets total strand concentration to conc.
-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.

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. vantHoff-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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