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).
-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)
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).
maskfeat is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.