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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).


Input section
-sequence seqall

Required section
-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.

Additional section
Product options
-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)

Thermodynamic options
-thermo toggle
Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data

-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.

Advanced section
-rna boolean
This specifies that the sequence is an RNA sequence and not a DNA sequence.

Output section
-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:

-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.

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