---
name: "glam2mask"
section: "1"
platform: "linux"
package: "glam2"
version: "1064-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/glam2mask"
---

# glam2mask(1)

masks a GLAM2 motif in sequences

## NAME

glam2mask - masks a GLAM2 motif in sequences

## SYNOPSIS

**glam2mask** \[**options**\] *my\_motif.glam2* *my\_seqs.fa*

## DESCRIPTION

**glam2mask** masks a **glam2** motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with the symbol ´x´. By alternately applying **glam2** and **glam2mask** several times, it is possible to find the strongest, second-strongest, third-strongest, etc. motifs in a set of sequences.

## OPTIONS (DEFAULT SETTINGS)

**-o**

Output file (*stdout*).

**-x**

Mask character (*x*).

## SEE ALSO

[**glam2format**(1)](/glam2format/1.md), [**glam2**(1)](/glam2/1.md), [**glam2-purge**(1)](/glam2-purge/1.md), [**glam2scan**(1)](/glam2scan/1.md)

The full Hypertext documentation of GLAM2 is available online at *http://bioinformatics.org.au/glam2/* or on this computer in */usr/share/doc/glam2/*.

## REFERENCE

If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).

## AUTHORS

**Martin Frith**

-

  Author of GLAM2.

**Timothy Bailey**

-

  Author of GLAM2.

**Charles Plessy** \<plessy@debian.org\>

-

  Formatted this manpage in DocBook XML for the Debian distribution.

## COPYRIGHT

The source code and the documentation of GLAM2 are released in the public domain.