sixpack1e
Display a dna sequence with 6-frame translation and orfs
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.