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

# sixpack(1e)

Display a DNA sequence with 6-frame translation and ORFs

## NAME

sixpack - Display a DNA sequence with 6-frame translation and ORFs

## SYNOPSIS

**sixpack** **-sequence** *sequence* \[**-table** *list*\] \[**-firstorf** *boolean*\] \[**-lastorf** *boolean*\] \[**-mstart** *boolean*\] **-outfile** *outfile* **-outseq** *seqoutall* **-reverse** *boolean* **-orfminsize** *integer* **-uppercase** *range* **-highlight** *range* **-number** *boolean* **-width** *integer* **-length** *integer* **-margin** *integer* **-name** *boolean* **-description** *boolean* **-offset** *integer* **-html** *boolean*

**sixpack** **-help**

## DESCRIPTION

**sixpack** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s).

## OPTIONS

### Input section

- **-sequence** *sequence*

  ### Additional section

- **-table** *list*

  Genetics code used for the translation

- **-firstorf** *boolean*

  Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. Default value: Y

- **-lastorf** *boolean*

  Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. Default value: Y

- **-mstart** *boolean*

  Displays only ORFs starting with an M. Default value: N

### Output section

- **-outfile** *outfile*

  - **-outseq** *seqoutall*

  ORF sequence output

- **-reverse** *boolean*

  Display also the translation of the DNA sequence in the 3 reverse frames Default value: Y

- **-orfminsize** *integer*

  Minimum size of Open Reading Frames (ORFs) to display in the translations. Default value: 1

- **-uppercase** *range*

  Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99

- **-highlight** *range*

  Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as '@filename'.

- **-number** *boolean*

  Number the sequence at the beginning and the end of each line. Default value: Y

- **-width** *integer*

  Number of nucleotides displayed on each line Default value: 60

- **-length** *integer*

  - **-margin** *integer*

  Default value: 10

- **-name** *boolean*

  Set this to be false if you do not wish to display the ID name of the sequence. Default value: Y

- **-description** *boolean*

  Set this to be false if you do not wish to display the description of the sequence. Default value: Y

- **-offset** *integer*

  Number from which you want the DNA sequence to be numbered. Default value: 1

- **-html** *boolean*

  Default value: N

## 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

sixpack 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.