maskfeat - Write a sequence with masked features

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EMBOSS 6.4.0                                       05/11/2012                                       MASKFEAT(1e)

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).

       maskfeat - Write a sequence with masked features

Inputsection-sequenceseqallAdditionalsection-typestring
           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*

       -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

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

maskfeat-sequenceseqall [-typestring] [-tolowertoggle] -maskcharstring-outseqseqoutmaskfeat-help