MOTIVATION: The numbers of finished and ongoing genome projects are increasing 
at a rapid rate, and providing the catalog of genes for these new genomes is a 
key challenge. Obtaining a set of well-characterized genes is a basic 
requirement in the initial steps of any genome annotation process. An accurate 
set of genes is needed in order to learn about species-specific properties, to 
train gene-finding programs, and to validate automatic predictions. 
Unfortunately, many new genome projects lack comprehensive experimental data to 
derive a reliable initial set of genes.
RESULTS: In this study, we report a computational method, CEGMA (Core Eukaryotic 
Genes Mapping Approach), for building a highly reliable set of gene annotations 
in the absence of experimental data. We define a set of conserved protein 
families that occur in a wide range of eukaryotes, and present a mapping 
procedure that accurately identifies their exon-intron structures in a novel 
genomic sequence. CEGMA includes the use of profile-hidden Markov models to 
ensure the reliability of the gene structures. Our procedure allows one to build 
an initial set of reliable gene annotations in potentially any eukaryotic 
genome, even those in draft stages.
AVAILABILITY: Software and data sets are available online at 
http://korflab.ucdavis.edu/Datasets.