---
name: "dan"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dan"
---

# dan(1e)

Calculates nucleic acid melting temperature

## 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.