This is the command dane that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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