RESEARCH PAPER
Annotating a non-model plant genome – a study on the narrow-leafed lupin

We present here a highly portable and easy-to-use gene annotation system CEL (Computational Environment for

annotation of Legume genomes) that can be used to annotate any type of genomic sequence -- from BAC ends to

complete chromosomes. CEL’s core engine is modular and hierarchically organized with an open-source structure,

permitting maximum customization -- users can assemble an individualized annotation pipeline by selecting

computational components that best suit their annotation needs. The tool is designed to speed up genomic analyses

and features an algorithm that substitutes for a biologist’s expertise at various steps of gene structure prediction.

This allows more complete automation of the labor-intensive and time-consuming annotation process.

The system collects and prioritizes multiple sources of de novo gene predictions and gene expression evidence

according to the confidence value of underlying supporting evidence, as a result producing high-quality genemodel

sets. The data produced by CEL pipeline is suitable for direct visualization in any genome browser tool that

supports GFF annotation format (e.g. Apollo, Artemis, Genome Browser etc.). This provides an easy means to

view and edit individual contigs and BACs using just mouse’s clicks and drag-and-drop features. Finally, we show

that CEL produces accurate annotations for novel draft genomes,of low quality or mostly non-existent, as in

the case of narrow-leafed lupin where the training-data are limited.