M i l e s to n e s

DOI: M iles tone 1 9 10.1038/nrg2243 The clickable

Consider a thought experiment in which the sequences of the human These heavily genome and the of several used genome model organisms were finished to a When the assembled draft a view of the genome at any scale, browsers are high standard, but the repositories sequence of the human genome and offers annotations in a series of now so much that were needed to house and make was published in February 2001, ‘tracks’ that can be added or elimi- sense of these data in an accessible it was made available through nated depending on the interests of a part of manner did not exist. The sequence three public portals: Ensembl, the the user. These heavily used genome the fabric of databases could be filled, but the University of California, Santa Cruz browsers are now so much a part of genome-based usefulness of the data to biologists (UCSC) Genome Browser and the the fabric of genome-based biologi- biological would be greatly diminished. In NCBI Map Viewer. Mainly funded cal research that their contribution place of a powerful resource, we by the Wellcome Trust, Ensembl to progress would be difficult to research would have an ‘alphabet soup’. is a joint project of the European overestimate. that their The earliest repositories for DNA Institute and the Alan Packer, Senior Editor, contribution to sequences established in the early- Wellcome Trust Sanger Institute. Nature Genetics to-mid 1980s were the European It presents a range of views of the ORIGINAL RESEARCH PAPERS Kent, W. J. et al. progress would Molecular Biology Laboratory human genome and the genomes The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002) | Birney, E. et al. An be difficult to Data Library, GenBank at the of an ever-increasing number of overview of Ensembl. Genome Res. 14, 925–928 overestimate. National Center for Biotechnology other organisms. Importantly, these (2004) Information (NCBI) and the DNA are ‘clickable’ genomes, so the user Further reading Reed, J. L., Famili, I. & Thiele, I. & Palsson, B.O. Towards Data Bank of Japan. Although can home in on small regions of a multidimensional genome annotation. Nature these databases have served the genome of interest to see protein- Rev. Genet. 7,130–141 (2006) | Eichler, E. E., Clark, R. A. & She, X. An assessment of the community admirably, as the pace coding genes, RNA-coding genes, sequence gaps: unfinished business in a finished of increased, it became single-nucleotide polymorphisms, human genome. Nature Rev. Genet. 5, 345–354 clear that new graphical user inter- nucleotide composition, pseudo- (2004) | Chintapalli, V.R., Wang, J. & Dow, J. A. Using FlyAtlas to identify better Drosophila faces would have to be developed in genes, contigs, expressed sequence melanogaster models of human disease. order to facilitate the viewing and tags, comparative alignments to Nature Genet. 39, 715–720 (2007) | Boffelli, D., manipulation of both the sequences other genomes and links to a suite Nobrega, M. A. & Rubin, E. M. Comparative at the vertebrate extremes. Nature Rev. and the subsequent annotations of other databases that constitute Genet.5, 456–465 (2004) | Ureta-Vidal, A., that would make them meaningful. the ongoing effort to produce a deep Ettwiller, L. & Birney, E. : genome-wide analysis in metazoan eukaryotes. An early and influential effort in functional annotation of sequenced Nature Rev. Genet. 4,251–262 (2003) this regard was ACeDB, a genomics genomes. The UCSC Genome WEB SITES database that was originally devel- Browser, which was produced in its DNA Data Bank of Japan: oped for the Caenorhabditis elegans initial form by the Santa Cruz group http://www.ddbj.nig.ac.jp Ensembl: http://www.ensembl.org that could display that carried out the first genome NCBI Map Viewer: http://www.ncbi.nlm.nih. genetic, cosmid and sequence maps assembly for the public Human gov/mapview in a flexible manner. Genome Project, can also present UCSC Genome Browser: http://www.genome.ucsc.edu

nature MILESTONES | DNA technologies november 2007 |  © 2007 Nature Publishing Group