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Annotating genomes with massive-scale RNA sequencing

France Denoeud123, Jean-Marc Aury123*, Corinne Da Silva123, Benjamin Noel123, Odile Rogier123, Massimo Delledonne4, Michele Morgante5, Giorgio Valle6, Patrick Wincker123, Claude Scarpelli123, Olivier Jaillon123 and François Artiguenave123

Author Affiliations

1 CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France

2 CNRS, UMR 8030, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France

3 Université d'Evry, 91057 Evry, France

4 Scientific and Technology Department, strada le Grazie 15, 37134 Verona, Italy

5 Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine, Via Linussio 51, 33100 Udine, Italy

6 CRIBI, Università degli Studi di Padova, viale G. Colombo, 35121 Padova, Italy

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Genome Biology 2008, 9:R175  doi:10.1186/gb-2008-9-12-r175

Published: 16 December 2008

Abstract

Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.