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EuGène
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.
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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EuGène graphical output |
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. There exists a large variety of plugins 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 "Annotastruct" 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). |
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EuGène has been used extensively on the
Arabidopsis
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 [Reference]. It has been adapted to
other plant and related
organims. EuGène has been developped with funding from
INRA and
Génoplante. The software is now OSI Certified Open Source Software under the terms of the Artistic License. |
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