title: The UCSC Genome Browser Database: update 2009.
abstract: The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate 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 Proteome Browser, VisiGene and Genome Graphs.
authors.affiliation: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. kuhn@soe.ucsc.edu
authors.forename: R M
authors.initials: RM
authors.lastname: Kuhn
authors.forename: D
authors.initials: D
authors.lastname: Karolchik
authors.forename: A S
authors.initials: AS
authors.lastname: Zweig
authors.forename: T
authors.initials: T
authors.lastname: Wang
authors.forename: K E
authors.initials: KE
authors.lastname: Smith
authors.forename: K R
authors.initials: KR
authors.lastname: Rosenbloom
authors.forename: B
authors.initials: B
authors.lastname: Rhead
authors.forename: B J
authors.initials: BJ
authors.lastname: Raney
authors.forename: A
authors.initials: A
authors.lastname: Pohl
authors.forename: M
authors.initials: M
authors.lastname: Pheasant
authors.forename: L
authors.initials: L
authors.lastname: Meyer
authors.forename: F
authors.initials: F
authors.lastname: Hsu
authors.forename: A S
authors.initials: AS
authors.lastname: Hinrichs
authors.forename: R A
authors.initials: RA
authors.lastname: Harte
authors.forename: B
authors.initials: B
authors.lastname: Giardine
authors.forename: P
authors.initials: P
authors.lastname: Fujita
authors.forename: M
authors.initials: M
authors.lastname: Diekhans
authors.forename: T
authors.initials: T
authors.lastname: Dreszer
authors.forename: H
authors.initials: H
authors.lastname: Clawson
authors.forename: G P
authors.initials: GP
authors.lastname: Barber
authors.forename: D
authors.initials: D
authors.lastname: Haussler
authors.forename: W J
authors.initials: WJ
authors.lastname: Kent
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D015870:Gene Expression; D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D012333:RNA, Messenger / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger