Scroll to navigation

MASKSEQ(1e) EMBOSS Manual for Debian MASKSEQ(1e)


maskseq - Write a sequence with masked regions


maskseq -sequence sequence -regions range [-tolower toggle] -maskchar  string -outseq seqout

maskseq -help


maskseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).


Input section

-sequence sequence

Required section

-regions range
Regions to mask. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99

Additional section

-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


Bugs can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


maskseq is fully documented via the tfm(1) system.


Debian Med Packaging Team <>
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.

05/11/2012 EMBOSS 6.4.0