Dispom - Revision history

Keilwagen at 08:23, 6 February 2015

Keilwagen — Fri, 06 Feb 2015 08:23:59 GMT

← Older revision		Revision as of 08:23, 6 February 2015
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	<!--__NOTOC__-->		<!--__NOTOC__-->
	by Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert and Ivo Grosse.		by Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert and Ivo Grosse.

			Recently, we published Dimont a successor of Dispom. Dimont uses some heuristics and is hence much faster than Dipom. Typically it provides results within one hour for large data sets. If you are interested in Dimont please visit the [[Dimont \| project homepage]].

	== Description ==		== Description ==

Grau: /* Download */

Grau — Tue, 14 Feb 2012 07:49:26 GMT

Download

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	''The original version of Dispom contained a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor (see documentation below), which can be used to predict binding sites given a trained classifier.''		''The original version of Dispom contained a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor (see documentation below), which can be used to predict binding sites given a trained classifier.''

	* Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom here].		* Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom1.1 here].
			* An alternative version adapted to Jstacs 2.0 can be downloaded [http://www.jstacs.de/download.php?which=Dispom here].
	* The benchmark data sets with implanted binding sites from [http://jaspar.cgb.ki.se/ Jaspar database] can be downloaded [http://www.jstacs.de/downloads/benchmark.zip here].		* The benchmark data sets with implanted binding sites from [http://jaspar.cgb.ki.se/ Jaspar database] can be downloaded [http://www.jstacs.de/downloads/benchmark.zip here].
	* The auxin data sets can be downloaded [http://www.jstacs.de/downloads/auxin.zip here].		* The auxin data sets can be downloaded [http://www.jstacs.de/downloads/auxin.zip here].

Grau at 10:22, 26 May 2011

Grau — Thu, 26 May 2011 10:22:13 GMT

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	<tr>		<tr>
	<td><font color="green">xml</font></td>		<td><font color="green">xml</font></td>
	<td>the file name of the xml file the classifier is written to, default = ./classifier.xml</td>		<td>the file name of the xml file the classifier has been written to, default = ./classifier.xml</td>
	<td>String</td>		<td>String</td>
	</tr>		</tr>

Grau at 10:21, 26 May 2011

Grau — Thu, 26 May 2011 10:21:45 GMT

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 == Download ==
-''The original version of Dispom contained a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor, which can be used to predict binding sites given a trained classifier.''
+''The original version of Dispom contained a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor (see documentation below), which can be used to predict binding sites given a trained classifier.''
 * Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom here].
@@ Line 170: / Line 170: @@
 * Once, we used '''init=enum-data=8'''.
 For predicting binding sites, we used '''p-val=1E-4'''.

Grau: /* Download */

Grau — Thu, 26 May 2011 10:18:09 GMT

Download

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	== Download ==		== Download ==
	The original version of Dispom ~~contain~~ a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor, which can be used to predict binding sites given a trained classifier.		''The original version of Dispom contained a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor, which can be used to predict binding sites given a trained classifier.''

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

Grau: /* Download */

Grau — Thu, 26 May 2011 10:17:49 GMT

Download

← Older revision		Revision as of 10:17, 26 May 2011
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	== Download ==		== Download ==
			The original version of Dispom contain a trivial bug that, unfortunately, prevented Dispom from predicting any binding sites. However, the training process was not affected by this bug and worked completely as expected. For convenience, the updated version of Dispom contains a second program called DispomPredictor, which can be used to predict binding sites given a trained classifier.

	* Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom here].		* Dispom can be downloaded [http://www.jstacs.de/download.php?which=Dispom here].
	* The benchmark data sets with implanted binding sites from [http://jaspar.cgb.ki.se/ Jaspar database] can be downloaded [http://www.jstacs.de/downloads/benchmark.zip here].		* The benchmark data sets with implanted binding sites from [http://jaspar.cgb.ki.se/ Jaspar database] can be downloaded [http://www.jstacs.de/downloads/benchmark.zip here].

Grau at 05:22, 17 May 2011

Grau — Tue, 17 May 2011 05:22:49 GMT

← Older revision		Revision as of 05:22, 17 May 2011
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	~~AFAIC that~~'s the ~~best aswner so far!~~		=== Initialization strategies===

			The following initialization strategies are available for Dispom (argument font color="green">init</font>, see above):
			* best-random=<number>: choose the best (according to conditional likelihood) among <number> different random initializations of the ZOOPS model
			* best-random-motif=<number>: choose the best among <number> different random initializations of the motif model
			* best-random-plugin=<number>: choose the best among <number> motif models, initialized from a randomly chosen substring of the target data
			* enum-all=<length>: choose the best among motif models, each initialized from one of all possible <length>-mers
			* enum-data=<length>: choose the best among motif models, each initialized from one of all <length>-mers present in the data (allows for greater <length> then enum-all without greatly increased runtime)
			* heuristic=<number>: use a heuristic based on the differential occurrence of similar k-mers in the target compared to the control data set
			* specific=<sequence or file of sequences>: initialize the motif model either from a single sequence, e.g. specific=ACGTACGT, or from a file containing a set of sequences

			If you have a rough guess of the motif you want to find, we recommend to use '''init=specific=<>''' with your guess as input sequence or file.

			Otherwise, if available computation time is rather limited, we recommend to start with '''init=heuristic=100''', and proceed with '''init=enum-data=6''' or '''init=enum-data=8''', i.e. initialize from 6 or 8-mers.

			If more computation time is available, several starts with '''init=best-random-plugin=100''' may lead to improved motifs. However, these come at the expense of computation time.

	== Case studies ==		== Case studies ==

Grau: Undo revision 390 by 88.191.118.7 (talk)

Grau — Wed, 11 May 2011 16:36:20 GMT

Undo revision 390 by 88.191.118.7 (talk)

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Grau: Undo revision 391 by 195.184.101.131 (talk)

Grau — Wed, 11 May 2011 16:36:02 GMT

Undo revision 391 by 195.184.101.131 (talk)

← Older revision		Revision as of 16:36, 11 May 2011
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	~~AKAIK you've~~ got ~~the anewsr~~ in one!		Youve got it in one. Couldnt have put it beettr.

Grau: Undo revision 395 by 202.64.130.26 (talk)

Grau — Wed, 11 May 2011 16:35:51 GMT

Undo revision 395 by 202.64.130.26 (talk)

← Older revision		Revision as of 16:35, 11 May 2011
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	~~Now I feel sutipd. That~~'~~s cleared it up for me~~		AKAIK you've got the anewsr in one!