NAME

       dan - Calculates nucleic acid melting temperature

SYNOPSIS

       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

DESCRIPTION

       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).

OPTIONS

   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
           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.

   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:
           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

       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).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       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.