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maskfeat - Write a sequence with masked features


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

maskfeat -help


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).


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

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