Skip Navigation

UCSC Genome Browser


NAR Molecular Biology Database Collection entry number 316
Rosenbloom, Kate; Armstrong, Joel; Barber, Galt; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy; Fujita, Pauline; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T.; Li, Chin; Miga, Karen; Nguyen, Ngan; Paten, Benedict; Raney, Brian; Smit, Arian; Speir, Matthew; Zweig, Ann; Haussler, David; Kuhn, Robert; Kent, W. James
1 Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA 2 Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA 3 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA 4 Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA

Database Description

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s Web-based tools – including Blat, the Table Browser, VisiGene, the Gene Sorter, Genome Graphs, and the Variant Annotation Integrator -- provide an integrated environment for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation ‘tracks’ for nearly 90 organisms, many with multiple assembly versions. Most genome assemblies offer mapping and sequence annotation tracks describing assembly, gap, and GC content, and alignments of mRNA, EST, and RefSeq data from GenBank. Some assemblies provide additional gene annotations and sequence alignments of selected species to facilitate comparative and evolutionary investigations. The heavily annotated human genome offers extensive conservation and evolutionary comparisons, a large collection of gene models, regulation, expression, epigenetics and tissue differentiation, variation, phenotype and disease association data, and text-mined data from publications. In addition to the native data sets local to the UCSC servers, the Genome Browser offers several options to users for viewing their own sequence and annotations: track and assembly data hubs, custom tracks, and sessions. The Genome Browser database and tools may also be installed on a local server for customized use. The full set of data, software tools, downloads, and documentation can be found on the Genome Browser website.

References

1. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
2. Meyer,L.R., Zweig,A.S., Hinrichs,A.S., Karolchik,D., Kuhn,R.M., Wong,M., Sloan,C.A., Rosenbloom,K.R., Roe,G., Rhead,B. et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res., 41, D64-69.
3. NCBI Resource Coordinators. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
4. Flicek,P., Ahmed,I., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S. et al. (2013) Ensembl 2013. Nucleic Acids Res., 41, D48-55.
5. Blanchette,M., Diallo,A.B., Green,E.D., Miller,W. and Haussler,D. (2007) Computational reconstruction of ancestral DNA sequences. In Murphy,W.J. (ed), Methods in Molecular Biology: Phylogenomics, Springer, New York, pp. 171-184.
6. Hsu,F., Kent,W.J., Clawson,H., Kuhn,R.M., Diekhans,M. and Haussler,D. (2006) The UCSC Known Genes. Bioinformatics, 22, 1036-1046.
7. Karolchik,D., Kuhn,R.M., Baertsch,R., Barber,G.P., Clawson,H., Diekhans,M., Giardine,B., Harte,R.A., Hinrichs,A.S., Hsu,F. et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res., 36, D773-779.
8. ENCODE Project Consortium, Dunham,I., Kundaje,A., Aldred,S.F., Collins,P.J., Davis,C.A., Doyle,F., Epstein,C.B., Frietze,S., Harrow,J. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
9. Mouse ENCODE Consortium, Stamatoyannopoulos,J.A., Snyder,M., Hardison,R., Ren,B., Gingeras,T., Gilbert,D.M., Groudine,M., Bender,M., Kaul,R. et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol., 13, 418.
10. Rosenbloom,K.R., Sloan,C.A., Malladi,V.S., Dreszer,T.R., Learned,K., Kirkup,V.M., Wong,M.C., Maddren,M., Fang,R., Heitner,S.G. et al. (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res., 41, D56-63.
11. Lindblad-Toh,K., Garber,M., Zuk,O., Lin,M.F., Parker,B.J., Washietl,S., Kheradpour,P., Ernst,J., Jordan,G., Mauceli,E. et al. (2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478, 476-482.
12. Pruitt,K.D., Harrow,J., Harte,R.A., Wallin,C., Diekhans,M., Maglott,D.R., Searle,S., Farrell,C.M., Loveland,J.E., Ruef,B.J. et al. (2009) The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res., 19, 1506.
13. Burge,S.W., Daub,J., Eberhardt,R., Tate,J., Barquist,L., Nawrocki,E.P., Eddy,S.R., Gardner,P.P. and Bateman,A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-232.
14. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
15. Harrow,J., Frankish,A., Gonzalez,J.M., Tapanari,E., Diekhans,M., Kokocinski,F., Aken,B.L., Barrell,D., Zadissa,A., Searle,S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
16. Fokkema,I.F., Taschner,P.E., Schaafsma,G.C., Celli,J., Laros,J.F. and den Dunnen,J.T. (2011) LOVD v.2.0: the next generation in gene variant databases. Hum Mutat., 32, 557-563.
17. Stenson,P.D., Mort,M., Ball,E.V., Howells,K., Phillips,A.D., Thomas,N.S. and Cooper,D.N. (2009) The Human Gene Mutation Database (HGMD®): 2008 Update. Genome Med., 1, 13.
18. The UniProt Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
19. 1000 Genomes Project Consortium, Abecasis,G.R., Auton,A., Brooks,L.D., DePristo,M.A., Durbin,R.M., Handsaker,R.E., Kang,H.M., Marth,G.T. and McVean,G.A. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56-65.
20. Paten,B., Earl,D., Nguyen,N., Diekhans,M., Zerbino,D. and Haussler,D. (2011) Cactus: Algorithms for genome multiple sequence alignment. Genome Res., 21, 1512-1528.
21. Barrett,T., Wilhite,S.E., Ledoux,P., Evangelista,C., Kim,I.F., Tomashevsky,M., Marshall,K.A., Phillippy,K.H., Sherman,P.M., Holko,M. et al. (2013) NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res., 41, D991-995.
22. Bernstein,B.E., Stamatoyannopoulos,J.A., Costello,J.F., Ren,B., Milosavljevic,A., Meissner,A., Kellis,M., Marra,M.A., Beaudet,A.L., Ecker,J.R. et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol., 28, 1045-1048.
23. Haeussler,M., Gerner,M. and Bergman,C.M. (2011) Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics, 27, 980-986.
24. Meyer,M., Kircher,M., Gansauge,M.T., Li,H., Racimo,F., Mallick,S., Schraiber,J.G., Jay,F., Prüfer,K., de Filippo,C. et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science, 338, 222-226.
25. McLaren,W., Pritchard,B., Rios,D., Chen,Y., Flicek,P. and Cunningham,F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. BMC Bioinformatics, 26, 2069-2070.
26. Raney,B.J., Dreszer,T.R., Barber,G.P., Clawson,H., Fujita,P.A., Wang,T., Karolchik,D. and Kent,W.J. (2013) Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics (in press).
27. Kent,W.J., Zweig,A.S., Barber,G., Hinrichs,A.S. and Karolchik,D. (2010) BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics, 26, 2204-2207.
28. Li,H., Handsaker,B., Wysoker,A., Fennell,T., Ruan,J., Homer,N., Marth,G., Abecasis,G., Durbin,R. and 1000 Genome Project Data Processing Subgroup. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
29. Danecek,P., Auton,A., Abecasis,G., Albers,C.A., Banks,E., DePristo,M.A., Handsaker,R.E., Lunter,G., Marth,G.T., Sherry,S.T. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
30. Adams,D., Altucci,L., Antonarakis,S.E., Ballesteros,J., Beck,S., Bird,A., Bock,C., Boehm,B., Campo,E., Caricasole,A. et al. (2012) BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol., 30, 224-226.
31. Liu,X., Jian,X. and Boerwinkle,E. (2013) dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Hum Mutat., 34, E2393-402. 32. Hickey,G., Paten,B., Earl,D., Zerbino,D. and Haussler,D. (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics, 29, 1341-1342.


Oxford University Press is not responsible for the content of external internet sites