Annotating genomes with massive-scale RNA sequencing

doi:10.1186/gb-2008-9-12-r175

Genome Biology

Volume 9
Issue 12

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Denoeud F
Aury JM
Da Silva C
Noel B
Rogier O
Delledonne M
Morgante M
Valle G
Wincker P
Scarpelli C
Jaillon O
Artiguenave F

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Denoeud F
Aury JM
Da Silva C
Noel B
Rogier O
Delledonne M
Morgante M
Valle G
Wincker P
Scarpelli C
Jaillon O
Artiguenave F
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Annotating genomes with massive-scale RNA sequencing

France Denoeud¹^,2^,3^* , Jean-Marc Aury¹^,2^,3^* , Corinne Da Silva¹^,2^,3 , Benjamin Noel¹^,2^,3 , Odile Rogier¹^,2^,3 , Massimo Delledonne⁴ , Michele Morgante⁵ , Giorgio Valle⁶ , Patrick Wincker¹^,2^,3 , Claude Scarpelli¹^,2^,3 , Olivier Jaillon¹^,2^,3 and François Artiguenave¹^,2^,3

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

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

³Université d'Evry, 91057 Evry, France

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

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

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

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R175doi:10.1186/gb-2008-9-12-r175


Published:	16 December 2008

Subject areas: Genome studies, Methods

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.