Identifying protein-coding genes in genomic sequences

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.This work was carried out as part of the BioSapiens project. The BioSapiens project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health", contract number LHSG-CT-2003-503265. AR, SA and RG also acknowledge support from grants U01HG003150 and U01HG003147 from the National Human Genome Research Institute, NIH. RG acknowledges support from grant BIO2006-03380 from the Spanish Ministry of Education and Science. AR and SA acknowledge support from the EU AnEUploidy project, and the NCCR Frontiers in Genetics. LP thanks the Hungarian National Office for Research and Technology for partial support under grant no. RET14/2005. JA's work is supported by the Wellcome Trust