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FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

Philippe Gouret1*, Vérane Vitiello1, Nathalie Balandraud1, André Gilles1, Pierre Pontarotti1 and Etienne GJ Danchin12

Author Affiliations

1 Phylogenomics Laboratory. EA 3781 EGEE (Evolution, Genome, Environment), Université de Provence, Case 36, Pl. V. Hugo, 13331 Marseille Cedex 03. France

2 AFMB-UMR 6098- CNRS - U1 - U2 Glycogenomics and Biomedical Structural Biology Case 932, 163 Avenue de Luminy 13288 Marseille cedex 09, France

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BMC Bioinformatics 2005, 6:198  doi:10.1186/1471-2105-6-198

Published: 5 August 2005

Abstract

Background

Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps.

Results

Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data.

Conclusion

The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.