dan - Calculates nucleic acid melting temperature
dan -sequence seqall
-windowsize integer
-shiftincrement integer
-dnaconc float
-saltconc float
[-product toggle]
-formamide float
-mismatch float
-prodlen integer
[-thermo toggle]
-temperature float
-rna boolean
-plot toggle
-mintemp float
-graph xygraph
-outfile report
dan -help
dan is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Nucleic:Properties,Nucleic:Composition" command group(s).
-windowsize integer
The values of melting point and other thermodynamic
properties of the sequence are determined by taking a short length of sequence
known as a window and determining the properties of the sequence in that
window. The window is incrementally moved along the sequence with the
properties being calculated at each new position. Default value: 20
-shiftincrement integer
This is the amount by which the window is moved at each
increment in order to find the melting point and other properties along the
sequence. Default value: 1
-dnaconc float
Default value: 50.
-saltconc float
Default value: 50.
-product toggle
This prompts for percent formamide, percent of mismatches
allowed and product length.
-formamide float
This specifies the percent formamide to be used in
calculations (it is ignored unless -product is used). Default value: 0.
-mismatch float
This specifies the percent mismatch to be used in
calculations (it is ignored unless -product is used). Default value: 0.
-prodlen integer
This specifies the product length to be used in
calculations (it is ignored unless -product is used). Default value:
$(windowsize)
-thermo toggle
Output the DeltaG, DeltaH and DeltaS values of the
sequence windows to the output data file.
-temperature float
If -thermo has been specified then this specifies the
temperature at which to calculate the DeltaG, DeltaH and DeltaS values.
Default value: 25.
-rna boolean
This specifies that the sequence is an RNA sequence and
not a DNA sequence.
-plot toggle
If this is not specified then the file of output data is
produced, else a plot of the melting point along the sequence is
produced.
-mintemp float
Enter a minimum value for the temperature scale (y-axis)
of the plot. Default value: 55.
-graph xygraph
-outfile report
If a plot is not being produced then data on the melting
point etc. in each window along the sequence is output to the file.
Bugs can be reported to the Debian Bug Tracking system
(http://bugs.debian.org/emboss), or directly to the EMBOSS developers
(http://sourceforge.net/tracker/?group_id=93650&atid=605031).
dan is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
This manual page was autogenerated from an Ajax Control Definition
of the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.