NAME

       maskseq - Write a sequence with masked regions

SYNOPSIS

       maskseq -sequence sequence -regions range [-tolower toggle] -maskchar string
               -outseq seqout

       maskseq -help

DESCRIPTION

       maskseq 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 sequence

   Required section
       -regions range
           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

   Additional section
       -tolower toggle
           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

       -maskchar string
           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)

   Output section
       -outseq seqout

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

       maskseq 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.