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.