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maskfeate - Online in the Cloud

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This is the command maskfeate that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


maskfeat - Write a sequence with masked features

SYNOPSIS


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 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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