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Genome Biol. 2008;9(12):R175. doi: 10.1186/gb-2008-9-12-r175. Epub 2008 Dec 16.

Annotating genomes with massive-scale RNA sequencing.

Author information

1
CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France. fdenoeud@genoscope.cns.fr

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.

PMID:
19087247
PMCID:
PMC2646279
DOI:
10.1186/gb-2008-9-12-r175
[Indexed for MEDLINE]
Free PMC Article

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