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 Bioinformatics
Unit Number:  Unit 1.4
DOI:  10.1002/0471250953.bi0104s40
Online Posting Date:  December, 2012
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Abstract

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. Bioinform. 40:1.4.1‐1.4.33. © 2012 by John Wiley & Sons, Inc.

Keywords: Genome Browser; Table Browser; human genome; genome analysis; comparative genomics; human variation; next‐generation 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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Materials

Basic Protocol 1: Using the UCSC Genome Browser

  Necessary Resources
  • 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 16.0 or higher (http://www.mozilla.org/firefox); Internet Explorer 7.0 or higher (http://www.microsoft.com/ie); Chrome 22.0 or higher (http://www.google.com/chrome/browser/); or Safari 5.1 or higher (http://www.apple.com/safari); browser must have cookies enabled
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Figures

Videos

Literature Cited

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   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.
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Key References
   Kent et al., 2002. See above.
  A description of the UCSC Genome Browser tool and the underlying conceptual and technical framework.
   Dreszer et al., 2012. See above.
  The 2012 update of Kent et al. () that includes software enhancements and additions, new genome assemblies, and new annotations.
Internet Resources
  http://genome.ucsc.edu
  The UCSC Genome Bioinformatics and Genome Browser home page.
  http://hgdownload.cse.ucsc.edu/downloads.html
  The UCSC Genome Browser downloads server.
  http://genome‐mysql.cse.ucsc.edu
  The Genome Browser public MySql server.
  http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
  The UCSC Genome Browser User's Guide.
  http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
  The UCSC Table Browser User's Guide.
  http://genome.ucsc.edu/goldenPath/help/customTrack.html
  Information for constructing and uploading a custom annotation track.
  http://genome.ucsc.edu/ENCODE/
  UCSC Genome Browser ENCODE portal.
  http://genomewiki.ucsc.edu
  User‐editable Web site for sharing information related to the browser.
  genome@soe.ucsc.edu
  Mailing list for questions and discussions about the browser software, database, and genome assemblies.
  genome-announce@soe.ucsc.edu
  Mailing list for announcements about releases of browser software and data, server maintenance, etc.
  genome-mirror@soe.ucsc.edu
  Mailing list for questions and discussion about mirroring the UCSC Genome Browser.
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