transeq - Translate nucleic acid sequences
transeq -sequence seqall
[-frame list]
[-table list]
[-regions range]
[-trim boolean]
[-clean boolean]
-alternative boolean
-outseq seqoutall
transeq -help
transeq is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Nucleic:Translation" command group(s).
-frame list
Default value: 1
-table list
-regions range
Regions to translate. If this is left blank, then the
complete sequence is translated. 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 Note: you should not try to
use this option with any other frame than the default, -frame=1
-trim boolean
This removes all 'X' and '*' characters from the right
end of the translation. The trimming process starts at the end and continues
until the next character is not a 'X' or a '*' Default value: N
-clean boolean
This changes all STOP codon positions from the '*'
character to 'X' (an unknown residue). This is useful because some programs
will not accept protein sequences with '*' characters in them. Default value:
N
-alternative boolean
The default definition of frame '-1' is the
reverse-complement of the set of codons used in frame 1. (Frame -2 is the set
of codons used by frame 2, similarly frames -3 and 3). This is a common
standard, used by the Staden package and other programs. If you prefer to
define frame '-1' as using the set of codons starting with the last codon of
the sequence, then set this to be true. 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).
transeq is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
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.