maskseq - Write a sequence with masked regions

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                                        MASKSEQ(1e)

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

       maskseq - Write a sequence with masked regions

Inputsection-sequencesequenceRequiredsection-regionsrange
           Regions to mask. 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

   Additionalsection-tolowertoggle
           The region can be 'masked' by converting the sequence characters to lower-case, some non-EMBOSS
           programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the
           case change. You might like to ensure that the whole sequence is in upper-case before masking the
           specified regions to lower-case by using the '-supper' flag. Default value: N

       -maskcharstring
           Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. If
           the mask character is set to be the SPACE character or a null character, then the sequence is
           'masked' by changing it to lower-case, just as with the '-lowercase' flag. Default value:
           @($(acdprotein)?X:N)

   Outputsection-outseqseqout

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

maskseq-sequencesequence-regionsrange [-tolowertoggle] -maskcharstring-outseqseqoutmaskseq-help