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SIXPACK(1e) EMBOSS Manual for Debian SIXPACK(1e)

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.
 
05/11/2012 EMBOSS 6.4.0