---
name: "maskseq"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/maskseq"
---

# maskseq(1e)

Write a sequence with masked regions

## 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*

  ## BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group\_id=93650&atid=605031).

## SEE ALSO

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

## AUTHOR

**Debian Med Packaging Team** \<debian-med-packaging@lists.alioth.debian.org\>

Wrote the script used to autogenerate this manual page.

## COPYRIGHT

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.