The UCSC Genome Browser: What Every Molecular Biologist Should Know

Mary E. Mangan1, Jennifer M. Williams1, Robert M. Kuhn2, Warren C. Lathe1

1 OpenHelix LLC, Bainbridge Island, Washington, 2 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 19.9
DOI:  10.1002/0471142727.mb1909s107
Online Posting Date:  July, 2014
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Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. Curr. Protoc. Mol. Biol. 107:19.9.1‐19.9.36. © 2014 by John Wiley & Sons, Inc.

Keywords: UCSC Genome Browser; primers; custom tracks; variations; SNP; comparative genomics; ENCODE

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Table of Contents

  • Introduction
  • Basic Protocol 1: Understanding Genomic Data and Features with the UCSC Genome Browser Gateway
  • Support Protocol 1: Explore the ENCODE Data for Potential Regulatory Elements in a Genomic Region of Interest
  • Support Protocol 2: Visualizing SNPs in a Gene of Interest
  • Alternate Protocol 1: Find an Evolutionarily Conserved Region Between Several Fish Species and Human and View the Multiple Sequence Alignment
  • Basic Protocol 2: Use the UCSC Genome Browser Table Browser to Query the Underlying Database and Download a List of SNPs in a Gene
  • Alternate Protocol 2: For a List of SNPs, Use the Table Browser to Find the Corresponding Genes
  • Alternate Protocol 3: Use the Table Browser to Find Functional Annotations for a List of Genes
  • Basic Protocol 3: Create a Simple Custom Track in the UCSC Genome Browser to Display Data
  • Basic Protocol 4: Display a Track Hub to View Data Hosted by Outside Parties
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

Literature Cited
  Bare, J.C., Koide, T., Reiss, D.J., Tenenbaum, D., and Baliga, N.S. 2010. Integration and visualization of systems biology data in context of the genome. BMC Bioinform. 11:382.
  Church, D.M., Schneider, V.A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H.C., Agarwala, R., McLaren, W.M., Ritchie, G.R.S., and Albracht, D. 2011. Modernizing reference genome assemblies. PLoS Biol. 9:e1001091
  Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. (dbSNP Build ID: 138). Available from:
  Di Bernardo, M.C., Crowther‐Swanepoel, D., Broderick, P., Webb, E., Sellick, G., Wild, R., Sullivan, K., Vijayakrishnan, J., Wang, Y., Pittman, A.M., Sunter, N.J., Hall, A.G., Dyer, M.J., Matutes, E., Dearden, C., Mainou‐Fowler, T., Jackson, G.H., Summerfield, G., Harris, R.J., Pettitt, A.R., Hillmen, P., Allsup, D.J., Bailey, J.R., Pratt, G., Pepper, C., Fegan, C., Allan, J.M., Catovsky, D., and Houlston, R.S. 2008. A genome‐wide association study identifies six susceptibility loci for chronic lymphocytic leukemia. Nat. Genet. 40:1204‐1210.
  Flicek, P., Ahmed, I., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., García‐Girón, C., Gordon, L., Hourlier, T., Hunt, S., Juettemann, T., Kähäri, A.K., Keenan, S., Komorowska, M., Kulesha, E., Longden, I., Maurel, T., McLaren, W.M., Muffato, M., Nag, R., Overduin, B., Pignatelli, M., Pritchard, B., Pritchard, E., Riat, H.S., Ritchie, G.R., Ruffier, M., Schuster, M., Sheppard, D., Sobral, D., Taylor, K., Thormann, A., Trevanion, S., White, S., Wilder, S.P., Aken, B.L., Birney, E., Cunningham, F., Dunham, I., Harrow, J., Herrero, J., Hubbard, T.J., Johnson, N., Kinsella, R., Parker, A., Spudich, G., Yates, A., Zadissa, A., and Searle, S.M. 2013. Ensembl 2013. Nucleic Acids Res. 41:D48‐D55.
  Haeussler, M., Gerner, M., and Bergman, C.M. 2011. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics 27:980‐986.
  Jeggari, A., Marks, D.S., and Larsson, E. 2012. miRcode: A map of putative microRNA target sites in the long non‐coding transcriptome. Bioinformatics 28:2062‐2063.
  Kuhn, R.M., Haussler, D., and Kent, W.J. 2013. The UCSC genome browser and associated tools. Brief Bioinform. 14:144‐161.
  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., Raney, B.J., Pohl, A., Malladi, V.S., Li, C.H., Lee, B.T., Learned, K., Kirkup, V., Hsu, F., Heitner, S., Harte, R.A., Haeussler, M., Guruvadoo, L., Goldman, M., Giardine, B.M., Fujita, P.A., Dreszer, T.R., Diekhans, M., Cline, M.S., Clawson, H., Barber, G.P., Haussler, D., and Kent, W.J. 2013. The UCSC Genome Browser database: Extensions and updates 2013. Nucleic Acids Res. 41:D64‐D69.
  NCBI Resource Coordinators. 2013. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41:D8‐D20.
  Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A., and Loraine, A.E. 2009. The Integrated Genome Browser: Free software for distribution and exploration of genome‐scale datasets. Bioinformatics 25:2730‐2731.
  Raney, B.J., Dreszer, T.R., Barber, G.P., Clawson, H., Fujita, P.A., Wang, T., Nguyen, N., Paten, B., Zweig, A.S., Karolchik, D., and Kent, W.J. 2013. Track Data Hubs enable visualization of user‐defined genome‐wide annotations on the UCSC Genome Browser. Bioinformatics 30:1003‐1005.
  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., Lee, B.T., Barber, G.P., Harte, R.A., Diekhans, M., Long, J.C., Wilder, S.P., Zweig, A.S., Karolchik, D., Kuhn, R.M., Haussler, D., and Kent, W.J. 2013. ENCODE data in the UCSC Genome Browser: Year 5 update. Nucleic Acids Res. 41:D56‐D63.
  Stein, L.D. 2013. Using GBrowse 2.0 to visualize and share next‐generation sequence data. Brief Bioinform. 14:162‐171.
  Thorvaldsdóttir, H., Robinson, J.T., and Mesirov, J.P. 2013. Integrative Genomics Viewer (IGV): High‐performance genomics data visualization and exploration. Brief Bioinform. 14:178‐192.
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