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<h1>GLAM2 Manual</h1>
<p><strong>Summary:</strong> GLAM2 is a software package for finding
<em>motifs</em> 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.</p>
<p><strong>Family:</strong> GLAM2 is a child of <a
href="http://zlab.bu.edu/glam/">GLAM</a> and a sibling of <a
href="ftp://ftp.ncbi.nih.gov/pub/spouge/papers/archive/AGLAM/">A-GLAM</a>.
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.</p>
<p<strong>Inventory:</strong> The package includes these programs:</p>
<ul>
<li><strong>glam2</strong> - for discovering motifs shared by a set of
sequences.</li>
<li><strong>glam2scan</strong> - for finding matches, in a sequence
database, to a motif discovered by glam2.</li>
<li><strong>glam2format</strong> - for converting glam2 motifs to
standard alignment formats.</li>
<li><strong>glam2mask</strong> - for masking glam2 motifs out of
sequences, so that weaker motifs can be found.</li>
<li><strong>purge</strong> - for removing highly similar members of a
set of sequences.</li>
</ul>
<p>These are <em>command line</em> 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.)</p>
<p><strong>About:</strong> GLAM2 was developed by <a
href="http://www.cbrc.jp/~martin/">Martin C Frith</a>, working at the
<a href="http://www.cbrc.jp/index.eng.html">Computational Biology
Research Center</a> in Tokyo, and <a
href="http://research.imb.uq.edu.au/~tbailey/">Timothy L Bailey</a>,
working at the <a href="http://www.imb.uq.edu.au/">Institute for
Molecular Bioscience</a> in Brisbane. The source code and
documentation are hereby released into the public domain. If you use
GLAM2, please cite:
<cite>MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering
sequence motifs with arbitrary insertions and deletions, PLoS
Computational Biology (in press)</cite>.</p>
<p><strong>Contact:</strong> 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.</p>
<h2>Contents</h2>
<ul>
<li><a href="install.html">Installation</a> - how to install GLAM2 on
your computer.</li>
<li><a href="glam2_tut.html">glam2 tutorial</a> - all you need to know
for typical usage of glam2.</li>
<li><a href="glam2_ref.html">glam2 reference</a> - all of glam2's
options.</li>
<li><a href="glam2scan.html">glam2scan manual</a></li>
<li><a href="glam2format.html">glam2format manual</a></li>
<li><a href="glam2mask.html">glam2mask manual</a></li>
<li><a href="purge.html">purge manual</a></li>
<li><a href="alphabet.html">Alphabets</a></li>
<li><a href="dirichlet.html">Dirichlet mixtures</a></li>
<li><a href="GLAM2_method.pdf">GLAM2 methods (PDF)</a> - mathematical
description of how GLAM2 works.</li>
</ul>
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