{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T18:42:35Z","timestamp":1775155355426,"version":"3.50.1"},"reference-count":57,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2009,12,15]],"date-time":"2009-12-15T00:00:00Z","timestamp":1260835200000},"content-version":"vor","delay-in-days":14,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CP in Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The University of California Santa Cruz (UCSC) Genome Browser is a popular Web\u2010based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation \u201ctracks.\u201d The annotations\u2014generated by the UCSC Genome Bioinformatics Group and external collaborators\u2014display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple\u2010species 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\u2010based application, the UCSC Table Browser. Users can upload data as custom annotation tracks in both browsers for research or educational use. 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. <jats:italic>Curr. Protoc. Bioinform<\/jats:italic>. 28:1.4.1\u20101.4.26. \u00a9 2009 by John Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/0471250953.bi0104s28","type":"journal-article","created":{"date-parts":[[2009,12,3]],"date-time":"2009-12-03T16:37:48Z","timestamp":1259858268000},"source":"Crossref","is-referenced-by-count":69,"title":["The UCSC Genome Browser"],"prefix":"10.1002","volume":"28","author":[{"given":"Donna","family":"Karolchik","sequence":"first","affiliation":[{"name":"Center for Biomolecular Science and Engineering, University of California Santa Cruz  Santa Cruz California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angie S.","family":"Hinrichs","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Science and Engineering, University of California Santa Cruz  Santa Cruz California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W. James","family":"Kent","sequence":"additional","affiliation":[{"name":"Center for Biomolecular Science and Engineering, University of California Santa Cruz  Santa Cruz California"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2009,12,15]]},"reference":[{"key":"e_1_2_7_2_1_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn665"},{"key":"e_1_2_7_2_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki135"},{"key":"e_1_2_7_2_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng0504-431"},{"key":"e_1_2_7_2_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0705-535"},{"key":"e_1_2_7_2_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn723"},{"key":"e_1_2_7_2_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.1.12"},{"key":"e_1_2_7_2_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn886"},{"key":"e_1_2_7_2_8_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1933104"},{"key":"e_1_2_7_2_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm881"},{"key":"e_1_2_7_2_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/35057192"},{"key":"e_1_2_7_2_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0209-153"},{"key":"e_1_2_7_2_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki057"},{"key":"e_1_2_7_2_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn842"},{"key":"e_1_2_7_2_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0091-679X(08)61405-3"},{"key":"e_1_2_7_2_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1105136"},{"key":"e_1_2_7_2_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm960"},{"key":"e_1_2_7_2_17_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2596504"},{"key":"e_1_2_7_2_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki100"},{"key":"e_1_2_7_2_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl048"},{"key":"e_1_2_7_2_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn828"},{"key":"e_1_2_7_2_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn785"},{"key":"e_1_2_7_2_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature02168"},{"key":"e_1_2_7_2_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04226"},{"key":"e_1_2_7_2_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg129"},{"key":"e_1_2_7_2_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh103"},{"key":"e_1_2_7_2_26_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229202"},{"key":"e_1_2_7_2_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.91"},{"key":"e_1_2_7_2_28_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.10.8.1115"},{"key":"e_1_2_7_2_29_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102"},{"key":"e_1_2_7_2_30_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1932072100"},{"key":"e_1_2_7_2_31_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3694705"},{"key":"e_1_2_7_2_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn875"},{"key":"e_1_2_7_2_33_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.199801"},{"key":"e_1_2_7_2_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj059"},{"key":"e_1_2_7_2_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn721"},{"key":"e_1_2_7_2_36_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.080531.108"},{"key":"e_1_2_7_2_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg050"},{"key":"e_1_2_7_2_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn741"},{"key":"e_1_2_7_2_39_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.809403"},{"key":"e_1_2_7_2_40_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3715005"},{"key":"e_1_2_7_2_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-437X(99)00031-3"},{"key":"e_1_2_7_2_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0962-8924(01)02104-3"},{"key":"e_1_2_7_2_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl1017"},{"key":"e_1_2_7_2_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn664"},{"key":"e_1_2_7_2_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01262"},{"key":"e_1_2_7_3_2_1","unstructured":"Kent et al. . See above."},{"key":"e_1_2_7_3_4_1","unstructured":"Kuhn et al. . See above."},{"key":"e_1_2_7_4_2_1","unstructured":"http:\/\/genome.ucsc.edu"},{"key":"e_1_2_7_4_4_1","unstructured":"http:\/\/hgdownload.cse.ucsc.edu\/downloads.html"},{"key":"e_1_2_7_4_6_1","unstructured":"http:\/\/genome\u2010mysql.cse.ucsc.edu"},{"key":"e_1_2_7_4_8_1","unstructured":"http:\/\/genome.ucsc.edu\/goldenPath\/help\/hgTracksHelp.html"},{"key":"e_1_2_7_4_10_1","unstructured":"http:\/\/genome.ucsc.edu\/goldenPath\/help\/hgTablesHelp.html"},{"key":"e_1_2_7_4_12_1","unstructured":"http:\/\/genome.ucsc.edu\/goldenPath\/help\/customTrack.html"},{"key":"e_1_2_7_4_14_1","unstructured":"http:\/\/genomewiki.ucsc.edu"},{"key":"e_1_2_7_4_16_1","unstructured":"genome@soe.ucsc.edu"},{"key":"e_1_2_7_4_18_1","unstructured":"genome-announce@soe.ucsc.edu"},{"key":"e_1_2_7_4_20_1","unstructured":"genome-mirror@soe.ucsc.edu"}],"container-title":["Current Protocols in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/0471250953.bi0104s28","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/0471250953.bi0104s28","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/0471250953.bi0104s28","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,20]],"date-time":"2023-08-20T20:12:19Z","timestamp":1692562339000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/0471250953.bi0104s28"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12]]},"references-count":57,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["10.1002\/0471250953.bi0104s28"],"URL":"https:\/\/doi.org\/10.1002\/0471250953.bi0104s28","archive":["Portico"],"relation":{},"ISSN":["1934-3396","1934-340X"],"issn-type":[{"value":"1934-3396","type":"print"},{"value":"1934-340X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,12]]}}}