D876–D882 Nucleic Acids Research, 2011, Vol. 39, Database issue doi:10.1093/nar/gkq963 Published online 18 October 2010 The UCSC Genome Browser database: update 2011 Pauline A. Fujita1,*, Brooke Rhead 1 , Ann S. Zweig1, Angie S. Hinrichs 1 , Donna Karolchik1, Melissa S. Cline 1 , Mary Goldman 1 , Galt P. Barber1, Hiram Clawson 1 , Antonio Coelho 1 , Mark Diekhans 1 , Timothy R. Dreszer1, Belinda M. Giardine 2 , Rachel A. Harte1, Jennifer Hillman-Jackson 1 , Fan Hsu 1 , Vanessa Kirkup 1 , Robert M. Kuhn 1 , Katrina Learned 1 , Chin H. Li1, Laurence R. Meyer1, Andy Pohl1,3, Brian J. Raney1, Kate R. Rosenbloom1, Kayla E. Smith1, David Haussler1,4 and W. James 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, USA, 3Centre for Genomic Regulation (CRG), Barcelona, Spain and 4Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA Received September 15, 2010; Accepted September 30, 2010 ABSTRACT The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks. INTRODUCTION The University of California, Santa Cruz (UCSC) Genome Browser provides online access to sequence and annotation data for the human genome and those of several other species (1,2). The level of annotation differs among species, with recent assemblies of the human genome being the most richly annotated. The Genome Browser contains mapping and sequencing annotation tracks describing assembly, gap and GC percent details for all assemblies. Most organisms also have tracks con- taining alignments of RefSeq genes (3,4), mRNAs and ESTs from GenBank (5) as well as gene and gene predic- tion tracks such as Ensembl Genes (6). UCSC Genes, a gene prediction track generated at UCSC that is based on data from RefSeq, GenBank, CCDS and UniProt (2,7,8), is present for the most recent human and mouse assemblies. Most organisms also have comparative genomic tracks showing pairwise genomic alignments between assemblies. Roughly half the organisms hosted in the browser have a multiple sequence alignment track (multiz) (9). Expression, regulation, variation and pheno- type tracks are available for many organisms. Track de- scriptions can be accessed by clicking on a track item, the track title or the vertical bar to the left of the track in the image. Links to the corresponding locations on the NCBI Map Viewer (10) and Ensembl (6) genome browsers are also provided. UCSC hosts the Data Coordination Center for the Encyclopedia of DNA Elements (ENCODE) project, using the Genome Browser website as its primary data portal (11–13). Genome-wide production phase data were initially published on the hg18 (NCBI build 36) human assembly and are currently being migrated to the hg19 (Genome Reference Consortium GRCh37) browser. (For more detail see Raney et al. in this issue.) The Genome Browser includes many tools for visualizing and analyzing genomic data. Sequence data *To whom correspondence should be addressed. Tel: +1 831 459 1477; Fax: +1 831 459 1809; Email: pauline@soe.ucsc.edu The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.