Introduction

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.

Download

At the moment, G-Mo.R-Se is still in development, but the current unstable version can be obtained from here.

Grapevine genome example

We demonstrate the feasibility of this method on the grapevine genome using ~175 million Solexa/Illumina RNA-Seq reads from four tissues. This allowed the identification of new exons (in known loci) and alternative splice forms, as well as entirely new loci. The G-Mo.R-Se models are available here. They can be visualized on the Vitis vinifera genome browser (tracks G-Mo.R-Se models). Solexa/Illumina reads can be downloaded from here.