maskseq1e
Write a sequence with masked regions
Usage
maskseq -sequence
sequence
-regions
range
[-tolower
toggle]
-maskchar
string
-outseq
seqout
maskseq -help
Overview
maskseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).
Options
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.