The human genome browser at UCSC

Genome Research
W James KentD Haussler

Abstract

As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site ...Continue Reading

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Dec 24, 2010·Nucleic Acids Research·Andreas ProkeschZlatko Trajanoski
Jan 21, 2011·Nucleic Acids Research·Motoharu OnoAngus I Lamond
May 4, 2010·Nucleic Acids Research·Yolande F M RamosPeter A C 't Hoen
May 21, 2010·Nucleic Acids Research·Eti MeiriEinat Sitbon
Jul 10, 2010·Nucleic Acids Research·Ekta KhuranaMark B Gerstein
Oct 12, 2010·Nucleic Acids Research·Andrew M ParrottMichael B Mathews
Oct 23, 2010·Nucleic Acids Research·Steven M GalloMarc S Halfon
Nov 17, 2011·Nucleic Acids Research·Riu YamashitaKenta Nakai
Nov 15, 2011·Nucleic Acids Research·Kate RosenbloomW James Kent
Nov 17, 2011·Nucleic Acids Research·Timothy R DreszerW James Kent
Nov 30, 2011·Nucleic Acids Research·Pascal GellertShizuka Uchida
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Dec 27, 2011·Nucleic Acids Research·Michelle S ScottAngus I Lamond
May 12, 2011·Nucleic Acids Research·Grace T HuangPanayiotis V Benos
May 18, 2011·Nucleic Acids Research·Jaebum Kim, Jian Ma
Jul 29, 2011·Nucleic Acids Research·Peter J ShepardKlemens J Hertel
Sep 24, 2011·Nucleic Acids Research·Ayana WienerMasha Y Niv
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Nov 15, 2011·Nucleic Acids Research·Patricia P ChanTodd M Lowe
Nov 22, 2011·Nucleic Acids Research·Thomas AbeelYves Van de Peer
Nov 17, 2012·Nucleic Acids Research·Laurence R MeyerW James Kent
Nov 30, 2012·Nucleic Acids Research·Jesse D ZiebarthYan Cui
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Dec 27, 2012·Nucleic Acids Research·Touati BenoukrafRichie Soong
Apr 19, 2012·Nucleic Acids Research·Sheroy MinocherhomjiAsli Silahtaroglu
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May 29, 2012·Nucleic Acids Research·Marc FiumeMichael Brudno
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Sep 4, 2012·Nucleic Acids Research·Zhen-Dong XiaoLiang-Hu Qu
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Jan 29, 2013·Nucleic Acids Research·Clayton K CollingsJohn N Anderson
Apr 20, 2013·Nucleic Acids Research·Charles D WardenYate-Ching Yuan
May 2, 2013·Nucleic Acids Research·Geir K SandveEivind Hovig
Jun 12, 2013·Nucleic Acids Research·Ignacio MedinaJoaquín Dopazo
Jul 31, 2004·Nucleic Acids Research·Marine Guillaud-BatailleGisèle Danglot
Feb 3, 2006·Nucleic Acids Research·Derek N FullerDouglas E Smith
Aug 11, 2012·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Laura AnesiUros Hladnik
Oct 19, 2010·Toxicological Sciences : an Official Journal of the Society of Toxicology·Shannon H O'SheaIvan Rusyn
Feb 13, 2009·Biology of Reproduction·Stephen T BradfordDagmar Wilhelm
Aug 31, 2012·Biology of Reproduction·Cherie M SouthwoodAlexander Gow
Aug 2, 2007·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Jonathan S BergSau Wai Cheung
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Feb 18, 2011·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Barry MooreMark Yandell
Nov 20, 2009·Clinical Dysmorphology·Jia-Chi Wang, Aneal Khan
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Mar 4, 2011·Psychiatric Genetics·Ney Alliey-RodriguezElliot S Gershon
Dec 28, 2012·Biology Letters·Philipp HohenbrinkUte Radespiel
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Feb 20, 2008·Genes & Development·Dana N LevasseurStuart H Orkin
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Feb 26, 2009·Genes & Development·Alena ShkumatavaDavid P Bartel
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