The UCSC Genome Browser

Donna Karolchik1, Angie S. Hinrichs1, W. James Kent1

1 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 18.6
DOI:  10.1002/0471142905.hg1806s71
Online Posting Date:  October, 2011
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The University of California Santa Cruz (UCSC) Genome Browser is a popular Web‐based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks.” The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple‐species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web‐based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks. Curr. Protoc. Hum. Genet. 71:18.6.1‐18.6.33 © 2011 by John Wiley & Sons, Inc.

Keywords: Genome Browser; Table Browser; human genome; genome analysis; comparative genomics; human variation; next‐gen sequencing; human genetics analysis; biological databases; BAM; bioinformatics; bioinformatics fundamentals

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Table of Contents

  • Introduction
  • Basic Protocol 1: Using the UCSC Genome Browser
  • Support Protocol 1: Creating a Custom Annotation Track
  • Support Protocol 2: Using the UCSC Table Browser
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Using the UCSC Genome Browser

  • Unix, Windows, or Macintosh workstation with an Internet connection and a minimum display resolution of 800 × 600 dpi
  • An up‐to‐date Internet browser that supports JavaScript, such as Firefox 3.0 or higher (; Internet Explorer 7.0 or higher (; or Safari 3.0 or higher (; browser must have cookies enabled

Support Protocol 1: Creating a Custom Annotation Track

  • Unix, Windows, or Macintosh workstation with an Internet connection and a minimum display resolution of 800 × 600 dpi
  • Text editor (Stein, )
  • An up‐to‐date Internet browser that supports JavaScript, such as Firefox 3.0 or higher (; Internet Explorer 7.0 or higher (; or Safari 3.0 or higher (; browser must have cookies enabled

Support Protocol 2: Using the UCSC Table Browser

  • Unix, Windows, or Macintosh workstation with an Internet connection and a minimum display resolution of 800 × 600 dpi
  • An up‐to‐date Internet browser that supports JavaScript, such as Firefox 3.0 or higher (; Internet Explorer 7.0 or higher (; or Safari 3.0 or higher (; browser must have cookies enabled
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Literature Cited

   1000 Genomes Project Consortium. 2010. A map of human genome variation from population‐scale sequencing. Nature. 467:1061‐1073.
   Amberger, J.S., Bocchini, C.A., Scott, A.F., and Hamosh, A. 2009. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 37:D793‐D796.
   Becker, K.G., Barnes, K.C., Bright, T.J., and Wang, S.A. 2004. The genetic association data6base. Nat. Genet. 36:431‐432.
   Bejerano, G., Siepel, A.C., Kent, W.J., and Haussler, D. 2005. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat. Methods 2:535‐545.
   Benson, D.A., Karsch‐Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. 2011. GenBank. Nucleic Acids Res. 39:D32‐D37.
   Benson, G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27:12‐17.
   Blake, J.A., Bult, C.J., Kadin, J.A., Richardson, J.E., Eppig, J.T., and the Mouse Genome Database Group. 2011. The Mouse Genome Database (MGD): Premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 39:D842‐D848.
   Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., and Miller, W. 2004. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14:708‐715.
   Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J. 2010. Galaxy: A web‐based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 89:19.10.1‐19.10.21.
   Borate, B. and Baxevanis, A.D. 2009. Searching online Mendelian Inheritance in Man (OMIM) for information on genetic loci involved in human disease. Curr. Protoc. Bioinform. 27:1.2.1‐1.2.13.
   Cheung, V.G., Nowak, N., Jang, W., Kirsch, I.R., Zhao, S., Chen, X.N., Furey, T.S., Kim, U.J., Kuo, W.L., and Livier, M. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409:953‐958.
   Cline, M.S. and Kent, W.J. 2009. Understanding genome browsing. Nat. Biotechnol. 27:153‐155.
   Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., Depristo, M.A., Handsaker, R., Lunter, G., Marth, G., Sherry, S.T., McVean, G., Durbin, R., and 1000 Genomes Project Analysis Group. 2011. The Variant Call Format and VCFtools. Bioinformatics. 27:2156‐2158.
   Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J.C., Hernandez‐Boussard, T., Rees, C.A., Cherry, J.M., Botstein, D., Brown, P.O., and Alizadeh, A.A. 2003. SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31:219‐223.
   Eeckman, F.H. and Durbin, R. 1995. ACeDB and Macace. Methods Cell Biol. 48:583‐605.
   The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636‐640.
   The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799‐816.
   Fernández‐Suárez, X.M. and Schuster, M.K. 2010. Using the Ensembl Genome server to browse genomic sequence data. Curr. Protoc. Bioinform. 30:1.15.1‐1.15.48.
   Finn, R.D., Mistry, J., Tate, J., Coggill, P.C., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E.L., Eddy, S.R., and Bateman, A. 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211‐D222.
   Firth, H.V., Richards, S.M., Bevan, A.P., Clayton, S., Corpas, M., Rajan, D., Van Vooren, S., Moreau, Y., Pettett, R.M., and Carter, N.P. 2009. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am. J. Hum. Genet. 84:524‐533.
   Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H.S., Rios, D., Ritchie, G.R., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y.A., Trevanion, S., Vandrovcova, J., Vilella, A.J., White, S., Wilder, S.P., Zadissa, A., Zamora, J., Aken, B.L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández‐Suarez, X.M., Herrero, J., Hubbard, T.J., Parker, A., Proctor, G., Vogel, J., and Searle, S.M. 2011. Ensembl 2011. Nucleic Acids Res. 39:D800‐D806.
   Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T.R., Giardine, B.M., Harte, R.A., Hillman‐Jackson, J., Hsu, F., Kirkup, V., Kuhn, R.M., Learned, K., Li, C.H., Meyer, L.R., Pohl, A., Raney, B.J., Rosenbloom, K.R., Smith, K.E., Haussler, D., and Kent, W.J. 2011. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res. 39:D876‐D882.
   Gibney, G. and Baxevanis, A.D. 2011. Searching NCBI databases using Entrez. Curr. Protoc. Bioinform. 34:1.3.1‐1.3.25.
   Goecks, J., Nekrutenko, A., Taylor, J., and The Galaxy Team. 2010. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11:R86.
   Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H., Hansen, N.F., Durand, E.Y., Malaspinas, A.S., Jensen, J.D., Marques‐Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H.A., Good, J.M., Schultz, R., Aximu‐Petri, A., Butthof, A., Höber, B., Höffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E.S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V.B., Golovanova, L.V., Lalueza‐Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R.W., Johnson, P.L., Eichler, E.E., Falush, D., Birney, E., Mullikin, J.C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., and Pääbo, S. 2010. A draft sequence of the Neandertal genome. Science. 328:710‐722.
   Harrow, J., Denoeud, F., Frankish, A, Reymond, A., Chen, C.K., Chrast, J., Lagarde, J., Gilbert, J.G., Storey, R., Swarbreck D., Rossier, C., Hubbard, T., Antonarakis, S.E., and Guigo, R. 2006. GENCODE: Producing a reference annotation for ENCODE. Genome Biol. 7:S4.1‐S4.9.
   Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S., and Manolio, T.A. 2009. Potential etiologic and functional implications of genome‐wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U.S.A. 106:9362‐9367.
   Hsu, F., Pringle, T.H., Kuhn, R.M., Karolchik, D., Diekhans, M., Haussler, D., and Kent, W.J. 2005. The UCSC Proteome Browser. Nucleic Acids Res. 33:D454‐D458.
   Hsu, F., Kent, W.J., Clawson, H., Kuhn, R.M., Diekhans, M., and Haussler, D. 2006. The UCSC known genes. Bioinformatics 22:1036‐1046.
   Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H., and Yeats, C. 2009. InterPro: The integrative protein signature database (2009). Nucleic Acids Res. 37:D224‐D228.
   The International HapMap Consortium. 2003. The International HapMap Project. Nature 426:789‐796.
   The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437:1299‐1320.
   The International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467:52‐58.
   Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., and Kent, W.J. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32:D493‐D496.
   Kent, W.J. 2002. BLAT–the BLAST‐like alignment tool. Genome Res. 12:656‐664.
   Kent, W.J. and Zahler, A.M. 2000a. The intronerator: Exploring introns and alternative splicing in C. elegans. Nucleic Acids Res. 28:91‐93.
   Kent, W.J. and Zahler, A.M. 2000b. Conservation, regulation, synteny, and introns in a large‐scale C. briggsae‐C. elegans genomic alignment. Genome Res. 10:1115‐1125.
   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.
   Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A. 100:11484‐11489.
   Kent, W.J., Hsu, F., Karolchik, D., Kuhn, R.M., Clawson, H., Trumbower, H., and Haussler, D. 2005. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 15:737‐741.
   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.
   Lein, E.S., Hawrylycz, M.J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A.F., Boguski, M.S., Brockway, K.S., Byrnes, E.J., Chen, L., Chen, L., Chen, T.M., Chin, M.C., Chong, J., Crook, B.E., Czaplinska, A., Dang, C.N., Datta, S., Dee, N.R., Desaki, A.L., Desta, T., Diep, E., Dolbeare, T.A., Donelan, M.J., Dong, H.W., Dougherty, J.G., Duncan, B.J., Ebbert, A.J., Eichele, G., Estin, L.K., Faber, C., Facer, B.A., Fields, R., Fischer, S.R., Fliss, T.P., Frensley, C., Gates, S.N., Glattfelder, K.J., Halverson, K.R., Hart, M.R., Hohmann, J.G., Howell, M.P., Jeung, D.P., Johnson, R.A., Karr, P.T., Kawal, R., Kidney, J.M., Knapik, R.H., Kuan, C.L., Lake, J.H., Laramee, A.R., Larsen, K.D., Lau, C., Lemon, T.A., Liang, A.J., Liu, Y., Luong, L.T., Michaels, J., Morgan, J.J., Morgan, R.J., Mortrud, M.T., Mosqueda, N.F., Ng, L.L, Ng, R., Orta, G.J., Overly, C.C., Pak, T.H., Parry, S.E., Pathak, S.D., Pearson, O.C., Puchalski, R.B., Riley, Z.L., Rockett, H.R., Rowland, S.A., Royall, J.J., Ruiz, M.J., Sarno, N.R., Schaffnit, K., Shapovalova, N.V., Sivisay, T., Slaughterbeck, C.R., Smith, S.C., Smith, K.A., Smith, B.I., Sodt, A.J., Stewart, N.N., Stumpf, K.R., Sunkin, S.M., Sutram, M., Tam, A., Teemer, C.D., Thaller, C., Thompson, C.L., Varnam, L.R., Visel, A., Whitlock, R.M., Wohnoutka, P.E., Wolkey, C.K., Wong, V.Y., Wood, M., Yaylaoglu, M.B., Young, R.C., Youngstrom, B.L., Yuan, X.F., Zhang, B., Zwingman, T.A., and Jones, A.R. 2007. Genome‐wide atlas of gene expression in the adult mouse brain. Nature. 445:168‐176.
   Lenhard, B., Hayes, W.S., and Wasserman, W.W. 2001. GeneLynx: A gene‐centric portal to the human genome. Genome Res. 11:2151‐2157.
   Leonard, S.A., Littlejohn, T.G., and Baxevanis, A.D. 2006. Common file formats. Curr. Protoc. Bioinform. 16:A.1B.1‐A.1B.9.
   Li, H. 2011. Tabix: Fast retrieval of sequence features from generic TAB‐delimited files. Bioinformatics 27:718‐719.
   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 (SAM) format and SAMtools. Bioinformatics 25:2078‐2079.
   Maglott, D., Ostell, J., Pruitt, K.D., and Tatusova, T. 2011. Entrez Gene: Gene‐centered information at NCBI. Nucleic Acids Res. 39:D52‐D57.
   Pieper, U., Webb, B.M., Barkan, D.T., Schneidman‐Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E.C., Pettersen, E.F., Huang, C.C., Datta, R.S., Sampathkumar, P., Madhusudhan, M.S., Sjölander, K., Ferrin, T.E., Burley, S.K., and Sali, A. 2011. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39:D465‐D474.
   Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R., and Siepel, A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20:110‐121.
   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., Hart, E., Suner, M.M., Landrum, M.J., Aken, B., Ayling, S., Baertsch, R., Fernandez‐Banet, J., Cherry, J.L., Curwen, V., Dicuccio, M., Kellis, M., Lee, J., Lin, M.F., Schuster, M., Shkeda, A., Amid, C., Brown, G., Dukhanina, O., Frankish, A., Hart, J., Maidak, B.L., Mudge, J., Murphy, M.R., Murphy, T., Rajan, J., Rajput, B., Riddick, L.D., Snow, C., Steward, C., Webb, D., Weber, J.A., Wilming, L., Wu, W., Birney, E., Haussler, D., Hubbard, T., Ostell, J., Durbin, R., and Lipman, D. 2009. The consensus coding sequence (CCDS) project: Identifying a common protein‐coding gene set for the human and mouse genomes. Genome Res. 19:1316‐1323.
   Raney, B.J., Cline, M.S., Rosenbloom, K.R., Dreszer, T.R., Learned, K., Barber, G.P., Meyer, L.R., Sloan, C.A., Malladi, V.S., Roskin, K.M., Suh, B.B., Hinrichs, A.S., Clawson, H., Zweig, A.S., Kirkup, V., Fujita, P.A., Rhead, B., Smith, K.E., Pohl, A., Kuhn, R.M., Karolchik, D., Haussler, D., and Kent, W.J. 2011. ENCODE whole‐genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 39:D871‐D875.
   Reese, M.G., Moore, B., Batchelor, C., Salas, F., Cunningham, F., Marth, G.T., Stein, L., Flicek, P., Yandell, M., and Eilbeck, K. 2010. A standard variation file format for human genome sequences. Genome Biol. 11:R88.
   Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D., Young, J., Yukich, B., Zardecki, C., Berman, H.M., and Bourne, P.E. 2011. The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Res. 39:D392‐D401.
   Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny‐Stein, T., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H., Sirota‐Madi, A., Olender, T., Golan, Y., Stelzer, G., Harel, A., and Lancet, D. 2010. GeneCards Version 3: The human gene integrator. Database (Oxford). 2010:baq020.
   Sanborn, J.Z., Benz, S.C., Craft, B., Szeto, C., Kober, K.M., Meyer, L., Vaske, C.J., Goldman, M., Smith, K.E., Kuhn, R.M., Karolchik, D., Kent, W.J., Stuart, J.M., Haussler, D., and Zhu, J. 2011. The UCSC Cancer Genomics Browser database: Update 2011. Nucleic Acids Res. 39:D951‐D959.
   Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S., Feolo, M., Fingerman, I.M., Geer, L.Y., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D.J., Lu, Z., Madden, T.L., Madej, T., Maglott, D.R., Marchler‐Bauer, A., Miller, V., Mizrachi, I., Ostell, J., Panchenko, A., Phan, L., Pruitt, K.D., Schuler, G.D., Sequeira, E., Sherry, S.T., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T.A., Wagner, L., Wang, Y., Wilbur, W.J., Yaschenko, E., and Ye, J. 2011. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39:D38‐D51.
   Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., Haussler, D., and Miller, W. 2003. Human‐mouse alignments with BLASTZ. Genome Res. 13:103‐107.
   Seal, R.L., Gordon, S.M., Lush, M.J., Wright, M.W., and Bruford, E.A. 2011. The HGNC resources in 2011. Nucleic Acids Res. 39:D514‐D519.
   Shimoyama, M., Smith, J.R., Hayman, T., Laulederkind, S., Lowry, T., Nigam, R., Petri, V., Wang, S.J., Dwinell, M., Jacob, H., and RGD Team. 2011. RGD: A comparative genomics platform. Hum. Genomics. 5:124‐129.
   Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R.K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034‐1050.
   Smit, A.F. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Gen. Dev. 9:657‐663.
   Stein, L.D. 2003. Creating databases for biological information: An introduction. Curr. Protoc. Bioinform. 00:9.1.1‐9.1.9.
   Stein L.D. 2006. Unix survival guide. Curr. Protoc. Bioinform. 00:16 A.1 C.1‐A.1 C.24.
   Strausberg, R.L., Greenhut, S.F., Grouse, L.H., Schaefer, C.F., and Buetow, K.H. 2001. In silico analysis of cancer through the Cancer Genome Anatomy Project. Trends Cell Biol. 11:S66‐S71.
   Su, A.I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K.A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., Cooke, M.P., Walker, J.R., and Hogenesch, J.B. 2004. A gene atlas of the mouse and human protein‐encoding transcriptomes. Proc. Natl. Acad. Sci. U.S.A. 101:6062‐6067.
   The UniProt Consortium. 2011. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39:D214‐D219.
   Wang, T. and Furey, T.S. 2009. Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. Circ. Cardiovasc. Genet. 2:199‐204.
   Waterston, R.H., Lindblad‐Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S.E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M.R., Brown, D.G., Brown, S.D., Bult, C., Burton, J., Butler, J., Campbell, R.D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A.T., Church, D.M., Clamp, M., Clee, C., Collins, F.S., Cook, L.L., Copley, R.R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K.D., Deri, J., Dermitzakis, E.T., Dewey, C., Dickens, N.J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D.M., Eddy, S.R., Elnitski, L., Emes, R.D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G.A., Flicek, P., Foley, K., Frankel, W.N., Fulton, L.A., Fulton, R.S., Furey, T.S., Gage, D., Gibbs, R.A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T.A., Green, E.D., Gregory, S., Guigo, R., Guyer, M., Hardison, R.C., Haussler, D., Hayashizaki, Y., Hillier, L.W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D.B., Johnson, L.S., Jones, M., Jones, T.A., Joy, A., Kamal, M., Karlsson, E.K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W.J., Kirby, A., Kolbe, D.L., Korf, I., Kucherlapati, R.S., Kulbokas, E.J., Kulp, D., Landers, T., Leger, J.P., Leonard, S., Letunic, I., Levine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D.R., Mardis, E.R., Matthews, L., Mauceli, E., Mayer, J.H., McCarthy, M., McCombie, W.R., McLaren, S., McLay, K., McPherson, J.D., Meldrim, J., Meredith, B., Mesirov, J.P., Miller, W., Miner, T.L., Mongin, E., Montgomery, K.T., Morgan, M., Mott, R., Mullikin, J.C., Muzny, D.M., Nash, W.E., Nelson, J.O., Nhan, M.N., Nicol, R., Ning, Z., Nusbaum, C., O'Connor, M.J., Okazaki, Y., Oliver, K., Overton‐Larty, E., Pachter, L., Parra, G., Pepin, K.H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C.S., Poliakov, A., Ponce, T.C., Ponting, C.P., Potter, S., Quail, M., Reymond, A., Roe, B.A., Roskin, K.M., Rubin, E.M., Rust, A.G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M.S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J.B., Slater, G., Smit, A., Smith, D.R., Spencer, B., Stabenau, A., Stange‐Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta‐Vidal, A., Vinson, J.P., Von Niederhausern, A.C., Wade, C.M., Wall, M., Weber, R.J., Weiss, R.B., Wendl, M.C., West, A.P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R.K., Winter, E., Worley, K.C., Wyman, D., Yang, S., Yang, S.P., Zdobnov, E.M., Zody, M.C., and Lander, E.S. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520‐562.
   Wilming, L.G., Gilbert, J.G., Howe, K., Trevanion, S., Hubbard, T., and Harrow, J.L. 2008. The vertebrate genome annotation (Vega) database. Nucleic Acids Res. 36:D753‐D760.
   Zhu, J., Sanborn, J.Z., Benz, S., Szeto, C., Hsu, F., Kuhn, R., Karolchik, D., Archie, J., Lenburg, M., Esserman, L., Kent, J., Haussler, D., and Wang, T. 2009. The UCSC Cancer Genomics Browser. Nat. Methods. 6:239‐240.
Key References
   Kent et al., 2002. See above.
  A description of the UCSC Genome Browser tool and the underlying conceptual and technical framework.
   Fujita et al., 2011. See above.
  The 2011 update of Kent et al. () that includes software enhancements and additions, new genome assemblies, and new annotations.
Internet Resources
  The UCSC Genome Bioinformatics and Genome Browser home page.
  The UCSC Genome Browser downloads server.
  The Genome Browser public MySql server.
  The UCSC Genome Browser User's Guide.
  The UCSC Table Browser User's Guide.
  Information for constructing and uploading a custom annotation track.
  UCSC Genome Browser ENCODE portal.
  User‐editable Website for sharing information related to the browser.
  Mailing list for questions and discussions about the browser software, database, and genome assemblies.
  Mailing list for announcements about releases of browser software and data, server maintenance, etc.
  Mailing list for questions and discussion about mirroring the UCSC Genome Browser.
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