maskfeat1e
Write a sequence with masked features
Usage
maskfeat -sequence
seqall
[-type
string]
[-tolower
toggle]
-maskchar
string
-outseq
seqout
maskfeat -help
Overview
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 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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.