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    <div class="memesuitelogo">
      <h1>The MEME Suite</h1>
      <h2>Motif-based sequence analysis tools</h2>
    </div>
    <h2>Frequently Asked Questions</h2>
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    <ul>
      <li> 
        <a href="#Q001"> <b>Q.</b> 
        I haven't received my MEME confirmation email?</a>
      </li> 
      <!--
      <li> 
        <a href="#Q002"> <b>Q.</b> 
        Is there a job queue that I can see how busy the cluster is?</a></li>
      -->
      <li> 
        <a href="#Q003"> <b>Q.</b> 
        Why don't the motif occurrences in the "Summary of Motifs" block diagrams match the occurrences shown in 
        the individual motif block diagrams?</a>
      </li> 
      <li> 
        <a href="#Q004"> <b>Q.</b> 
        MAST returns "Your sequence contains unrecognized characters..."</a>
      </li> 
      <li> 
        <a href="#Q005"> <b>Q.</b> 
        Is it possible to introduce specific amino acid
        compositions in the MEME and MAST programs?</a>
      </li> 
      <li>
        <a href="#Q006"> <b>Q.</b>
        I don't really understand what the pseudocount
        parameters for tomtom represent, nor how to use them
        properly.
      </li>
      <li>
        <a href="#Q007"> <b>Q.</b>
        MEME Suite won't compile!
        I get error messages about libxml2 or libxslt.
        What should I do?
      </li>
    </ul>
    <hr />
    <!-- Answers -->
    <ul>
      <li> 
        <a name="Q001"></a>
        <b>Q.</b> 
        I haven't received my MEME confirmation email?
        <p> 
        <b>A.</b> You should have received a
        confirmation email that your job is submitted.  If you
        haven't received this email, then you might have typed
        in the wrong email address.</p>
        <p>
        Alternatively, your mail program may be filtering the
        MEME emails as spam, so check your folders designated
        as junk e-mail or spam.  Try to configure your mail
        program not to filter out emails from
        <a href="mailto:@DEV_CONTACT@">@DEV_CONTACT@</a>.</p>
        <p>
        Please also check with your mail server administrator
        and see whether your email has been filtered out by
        spam filters run automatically on all incoming
        messages by your organization.</p>
        </p>
      </li>
    </ul>
    <hr />
    <ul>
      <li> 
        <a name="Q003"></a>
        <b>Q.</b> Why don't the motif occurrences in the
        "Summary of Motifs" block diagrams match the
        occurrences shown in the individual motif block
        diagrams?
        <p> 
        <b>A.</b> The motif occurrences shown for a motif in
        its section of the output are the ones discovered by
        the MEME algorithm.  These occurrences are then used
        to create a position specific scoring matrix (PSSM)
        for the motif.  The PSSMs for all of the motifs
        discovered by MEME are then used to search for
        non-overlapping sets of occurrences of motifs with
        p-values under 0.0001 using the MAST algorithm.  These
        are displayed in the "Summary of Motifs" block
        diagram.  Individual motif occurrences will sometimes
        be missing from the "Summary of Motifs" block diagram
        because of the non-overlapping or minimum p-value
        requirements.  Conversely, there may be motif
        occurrences in the summary diagram that were not
        discovered by the MEME algorithm.
        </p>
      </li>
    </ul>
    <hr />
    <ul>
      <li> 
        <a name="Q004"></a>
        <b>Q.</b> MAST returns "Your sequence contains
        unrecognized characters..."
        <p> 
        <b>A.</b> The file must be a plain text file. MSWord
        files, for example, are not acceptable. MSWord files
        can be converted to plain text by: <br/>
        "File"--&gt;"Save As"--&gt;"Save As Type"--&gt;"Plain Text'
        (*.txt)".
        </p>
      </li>
    </ul>
    <hr />
    <ul>
      <li>
        <a name="Q005"></a>
        <b>Q.</b> Is it possible to introduce specific amino
        acid compositions in the MEME and MAST programs?
        <p> 
        <b>A.</b> MEME can use higher-order background models.
        However, doing this requires a locally installed MEME
        and running "fasta-get-markov", which is included in
        the distribution. The relevant switch to MEME is
        "-bfile".</p>
        <p>
        MAST can only use zero-order (compositional)
        models. This is done automatically on the web server
        when searching the "upstream" databases using a file
        based on all upstream regions for the particular
        organism.  As with MEME, users of locally installed
        MAST can specify their own background files. The
        switch to MAST is "-bfile".
        </p> 
      </li>
    </ul>
    <hr/>
    <ul>
      <li>
        <a name="Q006"></a>
        <b>Q.</b>
        I don't really understand what the pseudocount
        parameters for tomtom represent, nor how to use them
        properly.
        <p>
        <b>A.</b> Essentially, a pseudocount corresponds to a
        Bayesian prior.  If you flip a coin 10 times and
        observe 10 heads in a row, then without a prior, you
        would estimate the probability of observing a heads on
        the next round as 100%.  But because you have a prior
        belief that the coin is probably fair, you might
        pretend that you started off with one heads and one
        tails.  Then you would say that you've seen 1 tails
        and 11 heads, so your probability of heads would be
        91.7%.  If you keep flipping the coin all day, and you
        only ever see heads, then the estimated probability of
        heads would eventually get very close to 100%.</p>

        <p>
        The motif pseudocounts work they same way: they allow
        you to say that, even though we've never seen an "A"
        in position 3 of the motif, it's still a possibility.
        Pseudocounts are important for motifs with few known
        occurrences.  If you have a motif built from 100
        instances, then the pseudocount is not likely to be
        important, but if the motif is based on only a handful
        of instances, then it is.</p>

        <p>
        Motifs coming out of MEME already have pseudocounts
        included in them.  Otherwise, it's a good idea to add
        a small pseudocount.</p>
      </li>
    </ul>
    <hr/>
    <ul>
      <li>
        <a name="Q007"></a>
        <b>Q.</b>
        MEME Suite won't compile!
        I get error messages about <code>libxml2</code> or <code>libxslt</code>.
        What should I do?
        <p>
        <b>A.</b>
        <a href="http://xmlsoft.org"><code>libxml2</code></a> 
        is a library for parsing XML files.
        <a href="http://xmlsoft.org/XSLT/"><code>libxslt</code></a> 
        is a library for processsing XML files.
        using XSLT stylesheets.
        MEME Suite will try to use the versions of these libraries
        already installed on your system. 
        If the libraries can't be found on your system, 
        MEME Suite will build its own copies from source included in the 
        MEME Suite distribution.
        If MEME Suite detects a local copy of <code>libxml2</code>, 
        but no local copy of <code>libxslt</code>, it will try to build
        its own copy of <code>libxslt</code>, but it may run into
        conflicts between the installed versions of <code>libxml2</code>
        and included version of <code>libxslt</code> that will keep MEME suite 
        from compiling.
        If you run into this problem you can force MEME Suite to build 
        both libraries from the included source.
        Just add the options <code>--enable-build-libxml2</code> and 
        <code>--enable-build-libxslt</code> to your <code>configure</code>
        command line.
        For further information about <code>configure</code> options see
        the <a href="install.html#customconfig">installation guide</a>.
        </p>
      </li>
    </ul>
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