MASKFEAT(1e) | EMBOSS Manual for Debian | MASKFEAT(1e) |
NAME¶
maskfeat - Write a sequence with masked featuresSYNOPSIS¶
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 seqallAdditional section¶
-type stringBy 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 seqoutBUGS¶
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.05/11/2012 | EMBOSS 6.4.0 |