---
name: "glam2scan"
section: "1"
platform: "linux"
package: "glam2"
version: "1064-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/glam2scan"
---

# glam2scan(1)

finds a GLAM2 motif in a database

## NAME

glam2scan - finds a GLAM2 motif in a database

## SYNOPSIS

**glam2scan** \[**options**\] **alphabet** *my\_motif.glam2* *my\_seqs.fa*

An alphabet other than *p* or *n* is interpreted as the name of an alphabet file.

## DESCRIPTION

**glam2scan** finds matches, in a sequence database, to a motif discovered by **glam2**. Each match receives a score, indicating how well it fits the motif.

## OPTIONS (DEFAULT SETTINGS)

**-h**

Show all options and their default settings.

**-o**

Output file (*stdout*).

**-n**

Number of alignments to report (*25*).

**-2**

Examine both strands - forward and reverse complement.

**-D**

Deletion pseudocount (*0.1*).

**-E**

No-deletion pseudocount (*2.0*).

**-I**

Insertion pseudocount (*0.02*).

**-J**

No-insertion pseudocount (*1.0*).

**-d**

Dirichlet mixture file.

## SEE ALSO

[**glam2format**(1)](/glam2format/1.md), [**glam2mask**(1)](/glam2mask/1.md), [**glam2-purge**(1)](/glam2-purge/1.md), [**glam2**(1)](/glam2/1.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.