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maskseqe - Online in the Cloud

Run maskseqe in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command maskseqe 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


maskseq - Write a sequence with masked regions

SYNOPSIS


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

maskseq -help

DESCRIPTION


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

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