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__NOTOC__
by Jens Keilwagen, Jan Baumbach, Thomas A. Kohl and Ivo Grosse.

== Description ==
Valuable binding site annotation data are stored in databases. However, several types of errors can, and do, occur in the process of manually incorporating annotation data from scientific literature into these databases. Here, we introduce MotifAdjuster, a software that helps to detect these errors, and we demonstrate its efficacy on public data sets.

== Paper ==
The paper [http://genomebiology.com/2009/10/5/R46/abstract '''''MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations'''''] has been published in [http://genomebiology.com/ Genome Biology].

== Download ==
MotifAdjuster can be downloaded [http://www.jstacs.de/download.php?which=MotifAdjuster here].

== Start instructions ==

If you have unzipped the archive, you can start the MotifAdjuster by invoking

<p><code>java -cp ./:./jstacs-1.2.2.jar:./numericalMethods.jar MotifAdjuster <font color="green">&lt;file&gt; &lt;ignoreChar&gt; &lt;length&gt; &lt;fgOrder&gt; &lt;fgEss&gt; &lt;bothStrands&gt; &lt;output&gt; &lt;sigma&gt; &lt;p(no motif)&gt;</font></code></p>

In Windows, you have to use &quot;;&quot; instead of &quot;:&quot; in the class path.

The arguments have the following meaning

<table border=0 cellpadding=10 align="center">
<tr>
	<td>name</td>
	<td>comment</td>
	<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr>
	<td><font color="green">file</font></td>
	<td>the location of the data set</td>
	<td>String</td>
</tr>
<tr>
	<td><font color="green">ignoreChar</font></td>
	<td>char for comment lines (e.g. for a FastA-file '&gt;')</td>
	<td>char</td>
</tr>
<tr>
	<td><font color="green">length</font></td>
	<td>the motif length</td>
	<td>int</td>
</tr>
<tr>
	<td><font color="green">fgOrder</font></td>
	<td>the order of the inhomogeneous Markov model that is uses for the motif; 0 yields in a PWM</td>
	<td>byte</td>
</tr>
<tr>
	<td><font color="green">ess</font></td>
	<td>the equivalent sample size that is used for the mixture model</td>
	<td>double &gt;= 0</td>
</tr>
<tr>
	<td><font color="green">bothStrands</font></td>
	<td>use both strands</td>
	<td>boolean</td>
</tr>
<tr>
	<td><font color="green">output</font></td>
	<td>output of the EM</td>
	<td>boolean</td></tr>
<tr>
	<td><font color="green">sigma</font></td>
	<td>the sigma of the truncated discrete Gaussian distribution</td>
	<td>double&gt;0</td>
</tr>
<tr>
	<td><font color="green">p(no motif)</font></td>
	<td>the probability for finding no motif</td>
	<td>0&lt;=double&lt;1</td>
</tr>
</table>


== Remark ==
The authors of [http://favorov.imb.ac.ru/SeSiMCMC/ SeSiMCMC] informed us that the performance of SeSiMCMC could be improved by using the latest version of SeSiMCMC (version 4.31 from 2009-04-23) and by using the advanced option ''Background model is common (static)'' set to the  value ''TRUE''. Hence, we provide an updated version of [http://www.jstacs.de/downloads/comparison_new.xls additional file 1].

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