title: The UCSC Genome Browser database: 2017 update.
abstract: Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA cath@ucsc.edu.
authors.forename: Cath
authors.initials: C
authors.lastname: Tyner
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Galt P
authors.initials: GP
authors.lastname: Barber
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Casper
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Eisenhart
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Clayton M
authors.initials: CM
authors.lastname: Fischer
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: David
authors.initials: D
authors.lastname: Gibson
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Jairo Navarro
authors.initials: JN
authors.lastname: Gonzalez
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Luvina
authors.initials: L
authors.lastname: Guruvadoo
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Haeussler
authors.affiliation: Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Heitner
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Angie S
authors.initials: AS
authors.lastname: Hinrichs
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Karolchik
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Brian T
authors.identifier: 0000-0001-6382-9738
authors.initials: BT
authors.lastname: Lee
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Christopher M
authors.identifier: 0000-0001-6382-9738
authors.initials: CM
authors.lastname: Lee
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Parisa
authors.initials: P
authors.lastname: Nejad
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Kate R
authors.initials: KR
authors.lastname: Rosenbloom
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Speir
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Villarreal
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: John
authors.initials: J
authors.lastname: Vivian
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Ann S
authors.initials: AS
authors.lastname: Zweig
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.|Howard Hughes Medical Institute, University of California Santa Cruz, CA 95064, USA.
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Kuhn
authors.affiliation: Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation; D057386:Search Engine; D012984:Software; D064878:Web Browser