application: maskfeat [ documentation: "Write a sequence with masked features" groups: "Edit, Feature tables" ] section: input [ information: "Input section" type: "page" ] seqall: sequence [ parameter: "Y" type: "any" features: "Y" ] endsection: input section: additional [ information: "Additional section" type: "page" ] string: type [ additional: "Y" default: "repeat*" information: "Type of feature to mask" help: "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://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt 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*" knowntype: "feature key list" ] toggle: tolower [ additional: "Y" default: "N" information: "Change masked region to lower-case" help: "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." ] string: maskchar [ additional: "@(!$(tolower))" default: "@($(acdprotein)?X:N)" information: "Character to mask with" maxlength: "1" help: "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." expected: "'X' for protein, 'N' for nucleic" knowntype: "sequence" ] endsection: additional section: output [ information: "Output section" type: "page" ] seqout: outseq [ parameter: "Y" ] endsection: output