Published online 7 November 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D755–D761 doi:10.1093/nar/gkn875 The UCSC Genome Browser Database: update 2009 R. M. Kuhn1,*, D. Karolchik1, A. S. Zweig1, T. Wang 1 , K. E. Smith1, K. R. Rosenbloom1, B. Rhead 1 , B. J. Raney1, A. Pohl1, M. Pheasant1, L. Meyer1, F. Hsu 1 , A. S. Hinrichs 1 , R. A. Harte1, B. Giardine 2 , P. Fujita1, M. Diekhans 1 , T. Dreszer1, H. Clawson 1 , G. P. Barber1, D. Haussler1,3 and W. J. Kent1 1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, 2Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and 3Howard Hughes Medical Institute, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA Received September 12, 2008; Revised October 16, 2008; Accepted October 17, 2008 ABSTRACT The UCSC Genome Browser Database (GBD, http:// genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and inte- grated annotations for a large number of organ- isms, including extensive comparative-genomic resources. In the past year, 13 new genome assem- blies have been added, including two important pri- mate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different verte- brates and 39 assemblies for 22 different inverte- brate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Pro- teome Browser, VisiGene and Genome Graphs. INTRODUCTION The UCSC Genome Browser Database (GBD, http:// genome.ucsc.edu) provides access to the DNA sequences for the human genome and many other organisms (1–4). The database also contains annotation datasets for a wide variety of data types aligned to the reference genome sequence, which are displayed graphically as ‘tracks’ in the UCSC Genome Browser. Currently, the GBD oﬀers sequence, annotations and browsers for 14 mammals, 10 nonmammalian vertebrates and 22 invertebrates, including 11 Drosophila species and six worms. Although we do not provide browsers for low-coverage assemblies, the GBD incorporates the sequences of bush- baby, treeshrew, rabbit, common shrew, hedgehog, arma- dillo, elephant and tenrec into the human and mouse comparative genomic annotations. We add new and updated assemblies to the database as they are released by the sequencing centers, and maintain older assem- blies either on the main site or in the genome archives (http://genome-archive.cse.ucsc.edu), where the complete history of the human genome sequence is available. Links to other major genome databases, including Ensembl (5) and NCBI MapViewer (6), are provided throughout the site. Genome assemblies are annotated with assembly clone details, GenBank mRNAs (7), RefSeq alignments (8), microarray gene expression data, regulatory element tracks, SNP and other variation data, multiple genome alignments and other datasets. The annotations oﬀered in the Genome Browser’s Comparative Genomics track group facilitate navigation among organisms using both the pairwise alignments in the chain and net tracks and multiple alignments (multiz) (9). Data in the GBD are updated regularly, including nightly updates of new mRNA submissions to GenBank (alignments of all new sequences to all assemblies), MGC (10) and consensus coding sequence (CCDS); weekly updates of EST data; and a complete realignment when- ever GenBank releases a periodic update. Certain other datasets are also updated regularly via new automated processes, including Ensembl genes annotations (5) on sev- eral organisms (updated 3–5 times a year), monthly updates of mouse data from the International Gene Trap Consortium (IGTC) (11) and regular new releases of the Database of Genomic Variants (DGV) (12). By providing up-to-date releases of data originated by other groups, along with convenient linkouts to the primary sources, we seek to maintain our database as an integrated resource *To whom correspondence should be addressed. Tel: +1 831 459 1487; Fax: +1 831 459 1809; Email: kuhn@soe.ucsc.edu 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.