dan - Calculates nucleic acid melting temperature

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       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
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EMBOSS 6.4.0                                       05/11/2012                                            DAN(1e)

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).

       dan - Calculates nucleic acid melting temperature

Inputsection-sequenceseqallRequiredsection-windowsizeinteger
           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

       -shiftincrementinteger
           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

       -dnaconcfloat
           Default value: 50.

       -saltconcfloat
           Default value: 50.

   AdditionalsectionProductoptions-producttoggle
           This prompts for percent formamide, percent of mismatches allowed and product length.

       -formamidefloat
           This specifies the percent formamide to be used in calculations (it is ignored unless -product is
           used). Default value: 0.

       -mismatchfloat
           This specifies the percent mismatch to be used in calculations (it is ignored unless -product is
           used). Default value: 0.

       -prodleninteger
           This specifies the product length to be used in calculations (it is ignored unless -product is used).
           Default value: $(windowsize)

   Thermodynamicoptions-thermotoggle
           Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file.

       -temperaturefloat
           If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG,
           DeltaH and DeltaS values. Default value: 25.

   Advancedsection-rnaboolean
           This specifies that the sequence is an RNA sequence and not a DNA sequence.

   Outputsection-plottoggle
           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.

       -mintempfloat
           Enter a minimum value for the temperature scale (y-axis) of the plot. Default value: 55.

       -graphxygraph-outfilereport
           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.

       dan is fully documented via the tfm(1) system.

dan-sequenceseqall-windowsizeinteger-shiftincrementinteger-dnaconcfloat-saltconcfloat
           [-producttoggle] -formamidefloat-mismatchfloat-prodleninteger [-thermotoggle]
           -temperaturefloat-rnaboolean-plottoggle-mintempfloat-graphxygraph-outfilereportdan-help