The UCSC Genome Browser database: update 2011

Pauline A. Fujita(University of California, Santa Cruz), Brooke Rhead(University of California, Santa Cruz), Ann S. Zweig(University of California, Santa Cruz), Angie S. Hinrichs(University of California, Santa Cruz), Donna Karolchik(University of California, Santa Cruz), Melissa Cline(University of California, Santa Cruz), Mary J. Goldman(University of California, Santa Cruz), G. P. Barber(University of California, Santa Cruz), Hiram Clawson(University of California, Santa Cruz), André Coelho(University of California, Santa Cruz), Mark Diekhans(University of California, Santa Cruz), Timothy R. Dreszer(University of California, Santa Cruz), Belinda Giardine(Pennsylvania State University), Rachel Harte(University of California, Santa Cruz), Jennifer Hillman‐Jackson(University of California, Santa Cruz), F. Hsu(University of California, Santa Cruz), Vanessa M. Kirkup(University of California, Santa Cruz), Robert M. Kuhn(University of California, Santa Cruz), Katrina Learned(University of California, Santa Cruz), Chunhao Li(University of California, Santa Cruz), Laurence Meyer(University of California, Santa Cruz), A. Pohl(Centre for Genomic Regulation), Brian J. Raney(University of California, Santa Cruz), Kate R. Rosenbloom(University of California, Santa Cruz), Kayla Smith(University of California, Santa Cruz), David Haussler(Howard Hughes Medical Institute), W. James Kent(University of California, Santa Cruz)
Nucleic Acids Research
October 18, 2010
10.1093/nar/gkq963
Cited by 1,869Open Access
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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.

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