The UCSC Genome Browser Database: update 2009

被引：281

作者：

Kuhn, R. M. ^{[1
]}

Karolchik, D. ^{[1
]}

Zweig, A. S. ^{[1
]}

Wang, T. ^{[1
]}

Smith, K. E. ^{[1
]}

Rosenbloom, K. R. ^{[1
]}

Rhead, B. ^{[1
]}

Raney, B. J. ^{[1
]}

Pohl, A. ^{[1
]}

Pheasant, M. ^{[1
]}

Meyer, L. ^{[1
]}

Hsu, F. ^{[1
]}

Hinrichs, A. S. ^{[1
]}

Harte, R. A. ^{[1
]}

Giardine, B. ^{[2
]}

Fujita, P. ^{[1
]}

Diekhans, M. ^{[1
]}

Dreszer, T. ^{[1
]}

Clawson, H. ^{[1
]}

Barber, G. P. ^{[1
]}

Haussler, D. ^{[1
,3
]}

Kent, W. J. ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Sch Engn, Santa Cruz, CA 95064 USA

[2] Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

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

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

关键词：

MOUSE; SEQUENCES; RESOURCE;

D O I：

10.1093/nar/gkn875

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：

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.

引用

页码：D755 / D761

页数：7

共 40 条

[1]

Acland A, 2013, NUCLEIC ACIDS RES, V41, pD8, DOI [10.1093/nar/gkx1095, 10.1093/nar/gks1189, 10.1093/nar/gkq1172]

[2] The universal protein resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Dobrokhotov, Pavel ;

Dornevil, Dolnide ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Ioannidis, Vassilios ;

Ivanyi, Ivan ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente ;

Lemercier, Philippe ;

Le Saux, Virginie .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D193-D197

[3] The BDGP gene disruption project: Single transposon insertions associated with 40% of Drosophila genes [J].

Bellen, HJ ;

Levis, RW ;

Liao, GC ;

He, YC ;

Carlson, JW ;

Tsang, G ;

Evans-Holm, M ;

Hiesinger, PR ;

Schulze, KL ;

Rubin, GM ;

Hoskins, RA ;

Spradling, AC .

GENETICS, 2004, 167 (02) :761-781

[4]

Benson DA, 2017, NUCLEIC ACIDS RES, V45, pD37, DOI [10.1093/nar/gkl986, 10.1093/nar/gkw1070, 10.1093/nar/gkg057, 10.1093/nar/gks1195, 10.1093/nar/gkp1024, 10.1093/nar/gkq1079, 10.1093/nar/gkr1202, 10.1093/nar/gkx1094, 10.1093/nar/gkn723]

[5] 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

[6] The HGNC Database in 2008: a resource for the human genome [J].

Bruford, Elspeth A. ;

Lush, Michael J. ;

Wright, Mathew W. ;

Sneddon, Tam P. ;

Povey, Sue ;

Birney, Ewan .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D445-D448

[7] The Mouse Genome Database (MGD): mouse biology and model systems [J].

Bult, Carol J. ;

Eppig, Janan T. ;

Kadin, James A. ;

Richardson, Joel E. ;

Blake, Judith A. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D724-D728

[8] The ENCODE (ENCyclopedia of DNA elements) Project [J].

Feingold, EA ;

Good, PJ ;

Guyer, MS ;

Kamholz, S ;

Liefer, L ;

Wetterstrand, K ;

Collins, FS ;

Gingeras, TR ;

Kampa, D ;

Sekinger, EA ;

Cheng, J ;

Hirsch, H ;

Ghosh, S ;

Zhu, Z ;

Pate, S ;

Piccolboni, A ;

Yang, A ;

Tammana, H ;

Bekiranov, S ;

Kapranov, P ;

Harrison, R ;

Church, G ;

Struhl, K ;

Ren, B ;

Kim, TH ;

Barrera, LO ;

Qu, C ;

Van Calcar, S ;

Luna, R ;

Glass, CK ;

Rosenfeld, MG ;

Guigo, R ;

Antonarakis, SE ;

Birney, E ;

Brent, M ;

Pachter, L ;

Reymond, A ;

Dermitzakis, ET ;

Dewey, C ;

Keefe, D ;

Denoeud, F ;

Lagarde, J ;

Ashurst, J ;

Hubbard, T ;

Wesselink, JJ ;

Castelo, R ;

Eyras, E ;

Myers, RM ;

Sidow, A ;

Batzoglou, S .

SCIENCE, 2004, 306 (5696) :636-640

[9] Ensembl 2008 [J].

Flicek, P. ;

Aken, B. L. ;

Beal, K. ;

Ballester, B. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cunningham, F. ;

Cutts, T. ;

Down, T. ;

Dyer, S. C. ;

Eyre, T. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. L. ;

Howe, K. ;

Johnson, N. ;

Jenkinson, A. ;

Kahari, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Prlic, A. ;

Rice, S. ;

Rios, D. ;

Schuster, M. ;

Sealy, I. ;

Slater, G. ;

Smedley, D. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. J. ;

Vogel, J. ;

White, S. ;

Wood, M. ;

Birney, E. ;

Cox, T. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D707-D714

[10] A second generation human haplotype map of over 3.1 million SNPs [J].

Frazer, Kelly A. ;

Ballinger, Dennis G. ;

Cox, David R. ;

Hinds, David A. ;

Stuve, Laura L. ;

Gibbs, Richard A. ;

Belmont, John W. ;

Boudreau, Andrew ;

Hardenbol, Paul ;

Leal, Suzanne M. ;

Pasternak, Shiran ;

Wheeler, David A. ;

Willis, Thomas D. ;

Yu, Fuli ;

Yang, Huanming ;

Zeng, Changqing ;

Gao, Yang ;

Hu, Haoran ;

Hu, Weitao ;

Li, Chaohua ;

Lin, Wei ;

Liu, Siqi ;

Pan, Hao ;

Tang, Xiaoli ;

Wang, Jian ;

Wang, Wei ;

Yu, Jun ;

Zhang, Bo ;

Zhang, Qingrun ;

Zhao, Hongbin ;

Zhao, Hui ;

Zhou, Jun ;

Gabriel, Stacey B. ;

Barry, Rachel ;

Blumenstiel, Brendan ;

Camargo, Amy ;

Defelice, Matthew ;

Faggart, Maura ;

Goyette, Mary ;

Gupta, Supriya ;

Moore, Jamie ;

Nguyen, Huy ;

Onofrio, Robert C. ;

Parkin, Melissa ;

Roy, Jessica ;

Stahl, Erich ;

Winchester, Ellen ;

Ziaugra, Liuda ;

Altshuler, David ;

Shen, Yan .

NATURE, 2007, 449 (7164) :851-U3

← 1 2 3 4 →