title: The UCSC Genome Browser database: extensions and updates 2011.
abstract: The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced 'track data hubs', which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.
authors.affiliation: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Dreszer
authors.forename: Donna
authors.initials: D
authors.lastname: Karolchik
authors.forename: Ann S
authors.initials: AS
authors.lastname: Zweig
authors.forename: Angie S
authors.initials: AS
authors.lastname: Hinrichs
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.forename: Robert M
authors.initials: RM
authors.lastname: Kuhn
authors.forename: Laurence R
authors.initials: LR
authors.lastname: Meyer
authors.forename: Mathew
authors.initials: M
authors.lastname: Wong
authors.forename: Cricket A
authors.initials: CA
authors.lastname: Sloan
authors.forename: Kate R
authors.initials: KR
authors.lastname: Rosenbloom
authors.forename: Greg
authors.initials: G
authors.lastname: Roe
authors.forename: Brooke
authors.initials: B
authors.lastname: Rhead
authors.forename: Andy
authors.initials: A
authors.lastname: Pohl
authors.forename: Venkat S
authors.initials: VS
authors.lastname: Malladi
authors.forename: Chin H
authors.initials: CH
authors.lastname: Li
authors.forename: Katrina
authors.initials: K
authors.lastname: Learned
authors.forename: Vanessa
authors.initials: V
authors.lastname: Kirkup
authors.forename: Fan
authors.initials: F
authors.lastname: Hsu
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Harte
authors.forename: Luvina
authors.initials: L
authors.lastname: Guruvadoo
authors.forename: Mary
authors.initials: M
authors.lastname: Goldman
authors.forename: Belinda M
authors.initials: BM
authors.lastname: Giardine
authors.forename: Pauline A
authors.initials: PA
authors.lastname: Fujita
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.forename: Melissa S
authors.initials: MS
authors.lastname: Cline
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.forename: Galt P
authors.initials: GP
authors.lastname: Barber
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: W
authors.initials: W
authors.lastname: James Kent
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D004194:Disease / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D010641:Phenotype
references.citation: Am J Hum Genet. 2009 Apr;84(4):524-33
references.pmid: 19344873
references.citation: PLoS Biol. 2010 Sep 07;8(9):
references.pmid: 20838655
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7
references.pmid: 21071399
references.citation: BMC Bioinformatics. 2008 Jul 22;9 Suppl 8:S3
references.pmid: 18673527
references.citation: Nature. 2005 Sep 1;437(7055):69-87
references.pmid: 16136131
references.citation: Bioinformatics. 2011 Mar 1;27(5):718-9
references.pmid: 21208982
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Nature. 1997 May 29;387(6632 Suppl):67-73
references.pmid: 9169866
references.citation: J Comput Biol. 2006 Mar;13(2):379-93
references.pmid: 16597247
references.citation: Nat Biotechnol. 2010 Oct;28(10):1045-8
references.pmid: 20944595
references.citation: Bioinformatics. 2010 Sep 1;26(17):2204-7
references.pmid: 20639541
references.citation: Nature. 2010 Oct 28;467(7319):1061-73
references.pmid: 20981092
references.citation: Bioinformatics. 2006 May 1;22(9):1036-46
references.pmid: 16500937
references.citation: Genome Biol. 2006;7 Suppl 1:S4.1-9
references.pmid: 16925838
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82
references.pmid: 20959295
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references.pmid: 11125122
references.citation: Nature. 2001 Feb 15;409(6822):934-41
references.pmid: 11237014
references.citation: Genome Res. 2005 Aug;15(8):1034-50
references.pmid: 16024819
references.citation: Genome Res. 2009 Jul;19(7):1316-23
references.pmid: 19498102
references.citation: Genome Res. 2004 Apr;14(4):708-15
references.pmid: 15060014
references.citation: Nature. 2011 Aug 31;477(7366):587-91
references.pmid: 21881562
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):38-41
references.pmid: 11752248
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6
references.pmid: 18842627
references.citation: Anim Genet. 2010 Oct;41(5):449-53
references.pmid: 20809919
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9
references.pmid: 18086701
references.citation: Genome Biol. 2009;10(4):R42
references.pmid: 19393038
references.citation: Bioinformatics. 2011 Aug 1;27(15):2156-8
references.pmid: 21653522
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6
references.pmid: 21045057
references.citation: PLoS Biol. 2011 Apr;9(4):e1001046
references.pmid: 21526222
references.citation: Bioinformatics. 2010 Jul 15;26(14):1772-6
references.pmid: 20547637
references.citation: Genome Res. 2010 Jan;20(1):110-21
references.pmid: 19858363
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5
references.pmid: 21037257
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712