# GLAM2 Manual

Summary: GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.

Family: GLAM2 is a child of GLAM and a sibling of A-GLAM. If you are looking for nucleotide motifs without insertions or deletions, A-GLAM is probably better. 'GLAM' used to stand for Gapless Local Alignment of Multiple sequences, but it now stands for Gapped Local Alignment of Motifs.

Inventory: The package includes these programs:

- glam2 - for discovering motifs shared by a set of sequences.
- glam2scan - for finding matches, in a sequence database, to a motif discovered by glam2.
- glam2format - for converting glam2 motifs to standard alignment formats.
- glam2mask - for masking glam2 motifs out of sequences, so that weaker motifs can be found.
- purge - for removing highly similar members of a set of sequences.

These are command line programs, so you need a basic familiarity with running things from your computer's command line in order to use them. (In Mac OS X, you want Applications -> Utilities -> Terminal.)

About: GLAM2 was developed by Martin C Frith, working at the Computational Biology Research Center in Tokyo, and Timothy L Bailey, working at the Institute for Molecular Bioscience in Brisbane. The source code and documentation are hereby released into the public domain. 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).

Contact: Questions and comments are welcome. Email: glam2(at-mark)imb.uq.edu.au. We would especially like to hear about any errors when installing or running the software (e.g. segmentation faults, assertion failures) so that we can fix them. Please send the exact text of the error message, and the exact inputs that produce the error.

## Contents

- Installation - how to install GLAM2 on your computer.
- glam2 tutorial - all you need to know for typical usage of glam2.
- glam2 reference - all of glam2's options.
- glam2scan manual
- glam2format manual
- glam2mask manual
- purge manual
- Alphabets
- Dirichlet mixtures
- GLAM2 methods (PDF) - mathematical description of how GLAM2 works.