sixpack (1e)

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

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).

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 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).

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

Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.

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.