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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta name="keywords" content="gene finding, gene prediction, integrative">
<title>EuGene : A Gene Finding Software</title>
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</head>
<body leftmargin="0" topmargin="0" marginwidth="0" marginheight="0"
bgcolor="white">
<script language="JavaScript1.2" src="Javascripts/euG_menu.js">
</script>
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<table height="100%" width="100%" CELLSPACING="0" CELLPADDING="0"
border="0" rows="2">
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<font color="#06768c"><b>EuGène</b></font>
is an open gene finder for eukaryotic
organisms. Compared to most existing gene finders,
EuGène is characterized by its ability to simply
integrate arbitrary sources of information in its
prediction process.
<br><br>
As most existing gene finders, EuGène can exploit
probabilistic models like Markov models for
discriminating coding from non coding sequences or
to discriminate effective splice sites from false
splice sites (using various mathematical models).
Beyond this EuGène is able to integrate information
from several signal (splice site, translation
start...) prediction software, similarity with
existing sequences (EST, mRNA, 5'/3' EST from full
length mRNA, proteins, genomic homologuous
sequences) and output of existing gene finders... Based on all the available information,
EuGène will output a prediction of maximal score i.e.,
maximally consistent with the information provided.
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<table CELLSPACING="0" CELLPADDING="2"
height="140" width="190" border="0">
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<td align="center" nowrap>
<font color="#c10505" size=-2>
<img src="Images/accoOn.jpg" height="15"
width="190" align="center">
<br><b>- N E W S -</b><br>
</font>
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<font size=-1 color="black">
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>
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>
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>
</font>
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<font color="#c10505" size="-2">
<img src="Images/spacer.jpg"
height="1" width="160">
<br><br><b>- L A S T U P D A T E
-</b><br>
</font>
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<font size=-1 color="black">
eugene v3.5g : Apr. 2009 <br>
eugene v3.5 : Sep. 2007<br>
eugene v3.4 : Dec. 2006<br>
eugene v3.3 : Sep. 2005<br>
eugene v3.2 : Apr. 2005<br>
eugene v3.1 : Feb. 2005<br>
eugene v3.0 : Oct. 2004<br>
EuGène Web : Aug. 21 2009
</font><br>
<img src="Images/accoOff.jpg" height="15"
width="190">
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<img src="Images/EugFig.png" width="400" vspace="10">
<br><font size=-1>EuGène graphical output</font>
</td>
<td colspan="2" align="justify">
Each source of information is integrated in EuGène
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 EuGène (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 EuGène's users have the
ability to extend EuGène. 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 EuGène 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 EuGène (without recompilation of
eugene).
</td>
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<td colspan="3" align="justify">
EuGène has been used extensively on the
<a href="orga_ara.html">Arabidopsis</a>
genome where it has shown its excellent prediction
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
organims. EuGène has been developped with funding from
<a href="http://www.inra.fr/">INRA</a> and
<a href="http://www.genoplante.com/htm/prehome.html">
Génoplante</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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