dan1e

Calculates nucleic acid melting temperature

Usage

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

Overview

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.

Releases

9 releases since Debian 5.0 (Lenny); the text changed 2 times.