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.