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.