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    <title>EuGene : A Gene Finding Software</title>
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		  <td colspan="2" valign="top" align="justify">
		    <font color="#06768c"><b>EuGne</b></font>
		    is an open gene finder for eukaryotic
		    organisms. Compared to most existing gene finders, 
		    EuGne is characterized by its ability to simply 
		    integrate arbitrary sources of information in its 
		    prediction process.
		    <br><br>
		    As most existing gene finders, EuGne can exploit 
		    probabilistic models like Markov models for 
		    discriminating coding from non coding sequences or 
		    to discriminate effective splice sites from false 
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		    splice sites (using various mathematical models). 
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		    Beyond this EuGne is able to integrate information 
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		    from several signal (splice site, translation
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		    start...) prediction software, similarity with 
		    existing sequences (EST, mRNA, 5'/3' EST from full 
		    length mRNA, proteins, genomic homologuous 
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		    sequences) and output of existing gene finders... Based on all the available information,
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		    EuGne will output a prediction of maximal score i.e.,
		    maximally consistent with the information provided.
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			      <br><b>-  N E W S  -</b><br>
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			    TAIR9 Genome Release [June 19, 2009] contains <br>EuGene
			    predictions (thanks to S. Aubourg, INRA-URGV)<br>
			      See JCVI [<a href="http://www.arabidopsis.org/news/news.jsp">news</a>]<br>
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			      Even more new A. thaliana genes predicted by<br> 
			      EuGene validated by RT-PCR<br>
			      See the [<a href="http://www.biomedcentral.com/1471-2164/8/401/abstract">paper</a>]<br>
			      Hundreds of new A. thaliana genes predicted by<br> 
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			      EuGene validated by RACEt<br> and included in TAIR 6 [<a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1783852">publication</a>]<br>
			      Developed using GForge: <a href=http://mulcyber.toulouse.inra.fr/projects/eugene>mulcyber</a><br>
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			    </font> 
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			      <br><br><b>-  L A S T  U P D A T E
				 -</b><br>
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			      eugene v3.5g : Apr. 2009 <br>
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			      eugene v3.5 : Sep. 2007<br>
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			      eugene v3.4 : Dec. 2006<br>
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			      eugene v3.3 : Sep. 2005<br>
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			      eugene v3.2 : Apr. 2005<br>
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			      eugene v3.1 : Feb. 2005<br>
			      eugene v3.0 : Oct. 2004<br>
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			      EuGne Web : Aug. 21 2009
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			    </font><br>
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		      <img src="Images/EugFig.png" width="400" vspace="10">
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		    <br><font size=-1>EuGne graphical output</font>
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		    Each source of information is integrated in EuGne
		    by a small independant software component, called
		    a "plugin". The plugin is responsible for the
		    integration of the information but also for
		    plotting the information on the graphical output
		    of EuGne (if needed) and can also analyze the
		    inconsistencies between the final prediction and
		    the information provided.  <br><br> There exists
		    a large variety of <a href="plugins.html">plugins</a>
		    currently but if needed EuGne's users have the
		    ability to extend EuGne. This can be done using
		    two different approaches. One simple approach is
		    to use the "<a
		    href="plugins.html#mixed_signal_content_plugins">Annotastruct</a>"
		    plugin.  This plugin allows to inject information
		    in EuGne using a GFF file. For the
		    more serious user, it is possible to write a new
		    plugin directly (in C++) and to load it
		    dynamically into EuGne (without recompilation of
		    eugene).
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		  </td>
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		    EuGne has been used extensively on the
		    <a href="orga_ara.html">Arabidopsis</a> 
		    genome where it has shown its excellent prediction 
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		    quality. Recent updates of TAIR include hundreds of new genes predicted by EuGene which have been validated by RACE by TIGR [<a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1783852">Reference</a>]. It has been adapted to 
		    <a href="organisms.html">other plant</a> and related 
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		    organims. EuGne has been developped with funding from
		    <a href="http://www.inra.fr/">INRA</a> and 
		    <a href="http://www.genoplante.com/htm/prehome.html">
		      Gnoplante</a>. <br>
		    The software is now OSI Certified Open Source Software under
		    the terms of the <a href="http://www.opensource.org/licenses/artistic-license.php">Artistic License</a>.
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