NAME

       trimseq - Remove unwanted characters from start and end of sequence(s)

SYNOPSIS

       trimseq -sequence seqall [-window integer] [-percent float] [-strict boolean] [-star boolean]
               -left boolean -right boolean -outseq seqoutall

       trimseq -help

DESCRIPTION

       trimseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It
       is part of the "Edit" command group(s).

OPTIONS

   Input section
       -sequence seqall

   Additional section
       -window integer
           This determines the size of the region that is considered when deciding whether the percentage of
           ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the
           sequence is shifted along the sequence from the ends and trimming is done only if there is a greater
           or equal percentage of ambiguity than the threshold percentage. Default value: 1

       -percent float
           This is the threshold of the percentage ambiguity in the window required in order to trim a sequence.
           Default value: 100.0

       -strict boolean
           In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M,
           R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. Default
           value: N

       -star boolean
           In protein sequences, trim off not only X's, but also the *'s Default value: N

   Advanced section
       -left boolean
           Default value: Y

       -right boolean
           Default value: Y

   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

       trimseq 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                                        TRIMSEQ(1e)