The UCSC Genome Browser database: 2015 update

被引：686

作者：

Rosenbloom, Kate R. ^{[1
]}

Armstrong, Joel ^{[1
]}

Barber, Galt P. ^{[1
]}

Casper, Jonathan ^{[1
]}

Clawson, Hiram ^{[1
]}

Diekhans, Mark ^{[1
]}

Dreszer, Timothy R. ^{[1
]}

Fujita, Pauline A. ^{[1
]}

Guruvadoo, Luvina ^{[1
]}

Haeussler, Maximilian ^{[1
]}

Harte, Rachel A. ^{[1
]}

Heitner, Steve ^{[1
]}

Hickey, Glenn ^{[1
]}

Hinrichs, Angie S. ^{[1
]}

Hubley, Robert ^{[2
]}

Karolchik, Donna ^{[1
]}

Learned, Katrina ^{[1
]}

Lee, Brian T. ^{[1
]}

Li, Chin H. ^{[1
]}

Miga, Karen H. ^{[1
]}

Nguyen, Ngan ^{[1
]}

Paten, Benedict ^{[1
]}

Raney, Brian J. ^{[1
]}

Smit, Arian F. A. ^{[2
]}

Speir, Matthew L. ^{[1
]}

Zweig, Ann S. ^{[1
]}

Haussler, David ^{[1
,3
]}

Kuhn, Robert M. ^{[1
]}

Kent, W. James ^{[1
]}

机构：

[1] UC Santa Cruz, CBSE, Santa Cruz, CA 95064 USA

[2] Inst Syst Biol, Seattle, WA 98109 USA

[3] UCSC, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

关键词：

SEQUENCE; ELEMENTS; REPEATS; ORIGIN; REFSEQ;

D O I：

10.1093/nar/gku1177

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (ext-link-type="uri" xlink:href="http://genome.ucsc.edu" xlink:type="simple">http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

引用

页码：D670 / D681

页数：12

共 60 条

[1]

Abecasis G.R., 2012, NATURE, V491, P56, DOI DOI 10.1038/nature11632

[2]

[Anonymous], NATURE

[3]

[Anonymous], PLOS CURR

[4] Ultraconserved elements in the human genome [J].

Bejerano, G ;

Pheasant, M ;

Makunin, I ;

Stephen, S ;

Kent, WJ ;

Mattick, JS ;

Haussler, D .

SCIENCE, 2004, 304 (5675) :1321-1325

[5]

Benson DA, 2007, NUCLEIC ACIDS RES, V35, pD21, DOI [10.1093/nar/gks1195, 10.1093/nar/gkp1024, 10.1093/nar/gkl986, 10.1093/nar/gkx1094, 10.1093/nar/gkw1070, 10.1093/nar/gkr1202, 10.1093/nar/gkn723, 10.1093/nar/gkg057, 10.1093/nar/gkq1079]

[6] Tandem repeats finder: a program to analyze DNA sequences [J].

Benson, G .

NUCLEIC ACIDS RESEARCH, 1999, 27 (02) :573-580

[7] The NIH Roadmap Epigenomics Mapping Consortium [J].

Bernstein, Bradley E. ;

Stamatoyannopoulos, John A. ;

Costello, Joseph F. ;

Ren, Bing ;

Milosavljevic, Aleksandar ;

Meissner, Alexander ;

Kellis, Manolis ;

Marra, Marco A. ;

Beaudet, Arthur L. ;

Ecker, Joseph R. ;

Farnham, Peggy J. ;

Hirst, Martin ;

Lander, Eric S. ;

Mikkelsen, Tarjei S. ;

Thomson, James A. .

NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048

[8] Aligning multiple genomic sequences with the threaded blockset aligner [J].

Blanchette, M ;

Kent, WJ ;

Riemer, C ;

Elnitski, L ;

Smit, AFA ;

Roskin, KM ;

Baertsch, R ;

Rosenbloom, K ;

Clawson, H ;

Green, ED ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2004, 14 (04) :708-715

[9] Prediction of complete gene structures in human genomic DNA [J].

Burge, C ;

Karlin, S .

JOURNAL OF MOLECULAR BIOLOGY, 1997, 268 (01) :78-94

[10] Rfam 11.0: 10 years of RNA families [J].

Burge, Sarah W. ;

Daub, Jennifer ;

Eberhardt, Ruth ;

Tate, John ;

Barquist, Lars ;

Nawrocki, Eric P. ;

Eddy, Sean R. ;

Gardner, Paul P. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D226-D232

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