sixpacke - Online in the Cloud

PROGRAM:

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

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