NAME

       transeq - Translate nucleic acid sequences

SYNOPSIS

       transeq -sequence seqall [-frame list] [-table list] [-regions range] [-trim boolean] [-clean boolean]
               -alternative boolean -outseq seqoutall

       transeq -help

DESCRIPTION

       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).

OPTIONS

   Input section
       -sequence seqall

   Additional section
       -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

   Advanced section
       -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

   Output section
       -outseq seqoutall

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

       transeq 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.

EMBOSS 6.4.0                                       05/11/2012                                        TRANSEQ(1e)