One of the major goals of Ensembl is to provide genesets which are as accurate and complete as possible and these continue to be used as reference genesets in analysis of new vertebrate genomes. Recent genome publications based on Ensembl genesets include those of Platypus Ornithorhynchus anatinus (11), the Oposum Monodelphis domestica (12) and the Rhesus Macaque Macaca mulatta (13). The gene build process is based on alignments of protein and cDNA sequences and there is continuous work to improve it and generate updated, more accurate and complete genesets. Different gene build strategies are used depending on the assembly, quality of the genome, its distance to high quality genomes and the extent of its organism-specific transcript evidence as has been previously described (18). This year one focus has been to develop a systematic post gene build comparative analysis process (using the Ensembl compara homology pipeline) to identify initial gene structures that appear to be evolutionarily inconsistent. These regions are then subject to a second, more computationally expensive localized gene build pipeline with more sensitive parameters. The major classes of problems
