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This site contains projects that use Jstacs. | This site contains projects that use Jstacs. | ||
= MotifAdjuster = | |||
by Jens Keilwagen, Jan Baumbach, Thomas 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 '''''MotifAdjuster: A tool for computational reassessment of transcription factor binding site annotations''''' has been submitted to [http://genomebiology.com/software/ Genome Biology]. | |||
== Download == | |||
MotifAdjuster download can be downloaded [http://www.jstacs.de/downloads/MotifAdjuster.zip here]. | |||
== Start instructions == | |||
If you have unzipped the archive, you can start the MotifAdjuster by invoking | |||
<p><code>java -cp ./:./jstacs-1.1.jar:./numericalMethods.jar MotifAdjuster <font color="green"><file> <ignoreChar> <length> <fgOrder> <fgEss> <bothStrands> <output> <sigma> <p(no motif)></font></code></p> | |||
In Windows, you have to use ";" instead of ":" 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 '>')</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 >= 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>0</td> | |||
</tr> | |||
<tr> | |||
<td><font color="green">p(no motif)</font></td> | |||
<td>the probability for finding no motif</td> | |||
<td>0<=double<1</td> | |||
</tr> | |||
</table> | |||
Revision as of 15:31, 30 October 2008
This site contains projects that use Jstacs.
MotifAdjuster
by Jens Keilwagen, Jan Baumbach, Thomas 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 MotifAdjuster: A tool for computational reassessment of transcription factor binding site annotations has been submitted to Genome Biology.
Download
MotifAdjuster download can be downloaded here.
Start instructions
If you have unzipped the archive, you can start the MotifAdjuster by invoking
java -cp ./:./jstacs-1.1.jar:./numericalMethods.jar MotifAdjuster <file> <ignoreChar> <length> <fgOrder> <fgEss> <bothStrands> <output> <sigma> <p(no motif)>
In Windows, you have to use ";" instead of ":" in the class path. The arguments have the following meaning
| name | comment | type |
| file | the location of the data set | String |
| ignoreChar | char for comment lines (e.g. for a FastA-file '>') | char |
| length | the motif length | int |
| fgOrder | the order of the inhomogeneous Markov model that is uses for the motif; 0 yields in a PWM | byte |
| ess | the equivalent sample size that is used for the mixture model | double >= 0 |
| bothStrands | use both strands | boolean |
| output | output of the EM | boolean |
| sigma | the sigma of the truncated discrete Gaussian distribution | double>0 |
| p(no motif) | the probability for finding no motif | 0<=double<1 |
