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

DebianMedPackagingTeam <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

       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).

       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)

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

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

Inputsection-sequenceseqallAdditionalsection-windowinteger
           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

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

       -strictboolean
           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

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

   Advancedsection-leftboolean
           Default value: Y

       -rightboolean
           Default value: Y

   Outputsection-outseqseqoutall

       trimseq is fully documented via the tfm(1) system.

trimseq-sequenceseqall [-windowinteger] [-percentfloat] [-strictboolean] [-starboolean]
               -leftboolean-rightboolean-outseqseqoutalltrimseq-help