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

# maskfeat(1e)

Write a sequence with masked features

## 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*

  ## 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

maskfeat 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.