NAME

       maskfeat - Write a sequence with masked features

SYNOPSIS

       maskfeat -sequence seqall [-type string] [-tolower toggle] -maskchar string -outseq seqout

       maskfeat -help

DESCRIPTION

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

OPTIONS

   Input section
       -sequence seqall

   Additional section
       -type string
           By default any feature in the feature table with a type starting 'repeat' is masked. You can set this
           to be any feature type you wish to mask. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the
           EMBL feature types and see Appendix A of the Swissprot user manual in
           http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types. The type may be
           wildcarded by using '*'. If you wish to mask more than one type, separate their names with spaces or
           commas, eg: *UTR repeat* Default value: repeat*

       -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

       maskfeat 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.