{"doi":"10.1002/0471250953.bi0104s17","title":"The UCSC Genome Browser","abstract":"<jats:title>Abstract</jats:title><jats:p>The University of California Santa Cruz (UCSC) Genome Browser (genome.ucsc.edu) 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—display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory 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 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:p>","journal":"Current Protocols in Bioinformatics","year":2007,"id":594391,"datarank":0.5289540786924243,"base_score":3.5263605246161616,"endowment":3.5263605246161616,"self_citation_contribution":0.5289540786924243,"citation_network_contribution":0.0,"self_endowment_contribution":0.5289540786924243,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":33,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":20036,"name":"Angie S. Hinrichs","orcid":"0000-0002-1697-1130","position":1,"is_corresponding":false},{"id":109839,"name":"W. James Kent","orcid":null,"position":2,"is_corresponding":false},{"id":20045,"name":"Donna Karolchik","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The UCSC Genome Browser","abstract":"<jats:title>Abstract</jats:title><jats:p>The University of California Santa Cruz (UCSC) Genome Browser (genome.ucsc.edu) 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—display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory 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 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:p>","is_dataset_classified":null,"base_score":3.5263605246161616,"endowment":3.5263605246161616,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"18428780","pmcid":null,"openalex_id":"https://openalex.org/W4230394123","authors":[],"funders":[{"funder_name":"Howard Hughes Medical Institute","grant_id":"","title":null}],"total_grants":1,"fwci":1.1992,"citation_percentile":0.78312834,"influential_citations":0,"citation_trend":[{"year":2012,"count":2},{"year":2013,"count":2},{"year":2014,"count":3},{"year":2016,"count":1},{"year":2017,"count":2},{"year":2018,"count":1},{"year":2019,"count":2},{"year":2020,"count":4},{"year":2022,"count":2},{"year":2024,"count":1},{"year":2025,"count":1}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1002/0471250953.bi0104s17","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1002/0471250953.bi0104s17","host_type":"publisher"},{"url":"https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/0471250953.bi0104s17","host_type":"publisher"},{"url":"https://doi.org/10.1002/0471250953.bi0104s17","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/18428780","host_type":"repository"}],"fields_of_study":["Genomics and Phylogenetic Studies","Gene expression and cancer classification","RNA modifications and cancer"],"mesh_terms":["Algorithms","Base Sequence","Chromosome Mapping","Computer Graphics","DNA","Molecular Sequence Data","Software","User-Computer Interface","Sequence Alignment","Sequence Analysis, DNA"],"keywords":["Genome browser","Upload","Annotation","Genome","Computer science","Genomics","Genome project","World Wide Web","Biology","Computational biology","Bioinformatics","Genetics","Gene"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-27T14:28:27.170869Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}