Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models.
First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.
G-Mo.R-Se is available at: http://www.genoscope.cns.fr/externe/gmorse/
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. (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9(12), R175. [abstract]