The UCSC Genome Browser database: 2023 update

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track...

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Vydané v:	Nucleic acids research Ročník 51; číslo D1; s. D1188 - D1195
Hlavní autori:	Nassar, Luis R, Barber, Galt P, Benet-Pagès, Anna, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S, Lee, Brian T, Lee, Christopher M, Muthuraman, Pranav, Nguy, Beagan, Pereira, Tiana, Nejad, Parisa, Perez, Gerardo, Raney, Brian J, Schmelter, Daniel, Speir, Matthew L, Wick, Brittney D, Zweig, Ann S, Haussler, David, Kuhn, Robert M, Haeussler, Maximilian, Kent, W James
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	England Oxford University Press 06.01.2023
Predmet:	COVID-19 - epidemiology COVID-19 - genetics Database Issue Databases, Genetic Genomics - methods Humans Internet Phylogeny SARS-CoV-2 - genetics Software Web Browser
ISSN:	0305-1048, 1362-4962, 1362-4962
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Abstract	The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
AbstractList	The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations. The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.
Author	Nassar, Luis R Benet-Pagès, Anna Fischer, Clay Nguy, Beagan Wick, Brittney D Haussler, David Lee, Brian T Kent, W James Gonzalez, Jairo Navarro Pereira, Tiana Zweig, Ann S Clawson, Hiram Hinrichs, Angie S Diekhans, Mark Schmelter, Daniel Perez, Gerardo Nejad, Parisa Speir, Matthew L Barber, Galt P Casper, Jonathan Muthuraman, Pranav Lee, Christopher M Haeussler, Maximilian Raney, Brian J Kuhn, Robert M
Author_xml	– sequence: 1 givenname: Luis R orcidid: 0000-0002-6706-2586 surname: Nassar fullname: Nassar, Luis R – sequence: 2 givenname: Galt P surname: Barber fullname: Barber, Galt P – sequence: 3 givenname: Anna surname: Benet-Pagès fullname: Benet-Pagès, Anna – sequence: 4 givenname: Jonathan surname: Casper fullname: Casper, Jonathan – sequence: 5 givenname: Hiram surname: Clawson fullname: Clawson, Hiram – sequence: 6 givenname: Mark orcidid: 0000-0002-0430-0989 surname: Diekhans fullname: Diekhans, Mark – sequence: 7 givenname: Clay surname: Fischer fullname: Fischer, Clay – sequence: 8 givenname: Jairo Navarro orcidid: 0000-0003-4022-4829 surname: Gonzalez fullname: Gonzalez, Jairo Navarro – sequence: 9 givenname: Angie S orcidid: 0000-0002-1697-1130 surname: Hinrichs fullname: Hinrichs, Angie S – sequence: 10 givenname: Brian T orcidid: 0000-0001-6382-9738 surname: Lee fullname: Lee, Brian T – sequence: 11 givenname: Christopher M orcidid: 0000-0001-6574-3567 surname: Lee fullname: Lee, Christopher M – sequence: 12 givenname: Pranav surname: Muthuraman fullname: Muthuraman, Pranav – sequence: 13 givenname: Beagan surname: Nguy fullname: Nguy, Beagan – sequence: 14 givenname: Tiana surname: Pereira fullname: Pereira, Tiana – sequence: 15 givenname: Parisa surname: Nejad fullname: Nejad, Parisa – sequence: 16 givenname: Gerardo surname: Perez fullname: Perez, Gerardo – sequence: 17 givenname: Brian J surname: Raney fullname: Raney, Brian J – sequence: 18 givenname: Daniel surname: Schmelter fullname: Schmelter, Daniel – sequence: 19 givenname: Matthew L orcidid: 0000-0002-2035-1129 surname: Speir fullname: Speir, Matthew L – sequence: 20 givenname: Brittney D surname: Wick fullname: Wick, Brittney D – sequence: 21 givenname: Ann S surname: Zweig fullname: Zweig, Ann S – sequence: 22 givenname: David surname: Haussler fullname: Haussler, David – sequence: 23 givenname: Robert M surname: Kuhn fullname: Kuhn, Robert M – sequence: 24 givenname: Maximilian surname: Haeussler fullname: Haeussler, Maximilian – sequence: 25 givenname: W James surname: Kent fullname: Kent, W James
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/36420891$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1093/nar/gkab996 10.1093/nar/gkaa1087 10.1038/s41586-022-04558-8 10.1101/gr.123356.111 10.1093/nar/gkab960 10.1093/bioinformatics/btl048 10.1093/nar/gkh103 10.1038/s41586-020-2876-6 10.1002/humu.24335 10.1093/bib/bbs017 10.1093/bioinformatics/btr330 10.1371/journal.pone.0170365 10.1093/nar/gkv1189 10.1101/gr.266932.120 10.1093/nar/29.1.308 10.1038/s41586-018-0590-4 10.1126/science.aaz1776 10.1016/j.ajhg.2009.03.010 10.1093/nar/gks1195 10.1101/gr.229102 10.1093/nar/gkab959 10.1038/s41588-021-00862-7 10.1093/nar/gkac238 10.1093/molbev/msab264 10.1093/bioinformatics/btq351 10.1016/j.gim.2022.04.017 10.1038/s41586-020-2871-y 10.1093/ve/veab064 10.1186/s13059-016-0924-1 10.1126/science.abj6987 10.1093/bioinformatics/btab503 10.1093/nar/gkab1049
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References	Armstrong (2023010804300289000_B25) 2020; 587 McBroome (2023010804300289000_B31) 2021; 38 Pavan (2023010804300289000_B14) 2017; 12 O’Toole (2023010804300289000_B30) 2021; 7 Lee (2023010804300289000_B7) 2021; 50 Kent (2023010804300289000_B8) 2010; 26 Kent (2023010804300289000_B1) 2002; 12 DiStefano (2023010804300289000_B15) 2022; 24 Sherry (2023010804300289000_B16) 2001; 29 Benson (2023010804300289000_B33) 2013; 41 Firth (2023010804300289000_B13) 2009; 84 Danecek (2023010804300289000_B9) 2011; 27 Karolchik (2023010804300289000_B11) 2004; 32 Yates (2023010804300289000_B36) 2020; 48 Li (2023010804300289000_B4) 2022; 50 Morales (2023010804300289000_B22) 2022; 604 Nurk (2023010804300289000_B34) 2022; 376 Buels (2023010804300289000_B5) 2016; 17 Turakhia (2023010804300289000_B29) 2021; 53 Frankish (2023010804300289000_B20) 2021; 49 Rangwala (2023010804300289000_B6) 2021; 31 Speir (2023010804300289000_B18) 2021; 37 Schaum (2023010804300289000_B19) 2018; 562 O’Leary (2023010804300289000_B21) 2016; 44 Paten (2023010804300289000_B26) 2011; 21 Hsu (2023010804300289000_B23) 2006; 22 Hammal (2023010804300289000_B32) 2021; 50 Cezard (2023010804300289000_B24) 2021; 50 Zoonomia Consortium (2023010804300289000_B27) 2020; 587 The GTEx Consortium (2023010804300289000_B28) 2020; 369 Benet-Pagès (2023010804300289000_B17) 2022; 43 Lee (2023010804300289000_B10) 2020; 48 Kent (2023010804300289000_B12) 2002; 12 Cunningham (2023010804300289000_B2) 2022; 50 Thorvaldsdóttir (2023010804300289000_B3) 2013; 14 Nair (2023010804300289000_B35) 2022
References_xml	– volume: 50 start-page: D316 year: 2021 ident: 2023010804300289000_B32 article-title: ReMap 2022: a database of human, mouse, drosophila and arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab996 – volume: 49 start-page: D916 year: 2021 ident: 2023010804300289000_B20 article-title: gencode 2021 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkaa1087 – volume: 604 start-page: 310 year: 2022 ident: 2023010804300289000_B22 article-title: A joint NCBI and EMBL-EBI transcript set for clinical genomics and research publication-title: Nature doi: 10.1038/s41586-022-04558-8 – volume: 21 start-page: 1512 year: 2011 ident: 2023010804300289000_B26 article-title: Cactus: algorithms for genome multiple sequence alignment publication-title: Genome Res. doi: 10.1101/gr.123356.111 – volume: 50 start-page: D1216 year: 2021 ident: 2023010804300289000_B24 article-title: The european variation archive: a FAIR resource of genomic variation for all species publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab960 – volume: 48 start-page: D756 year: 2020 ident: 2023010804300289000_B10 article-title: UCSC genome browser enters 20th year publication-title: Nucleic Acids Res. – volume: 22 start-page: 1036 year: 2006 ident: 2023010804300289000_B23 article-title: The UCSC known genes publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl048 – volume: 32 start-page: D493 year: 2004 ident: 2023010804300289000_B11 article-title: The UCSC table browser data retrieval tool publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh103 – volume: 587 start-page: 240 year: 2020 ident: 2023010804300289000_B27 article-title: A comparative genomics multitool for scientific discovery and conservation publication-title: Nature doi: 10.1038/s41586-020-2876-6 – volume: 43 start-page: 998 year: 2022 ident: 2023010804300289000_B17 article-title: Variant interpretation: UCSC genome browser recommended track sets publication-title: Hum. Mutat. doi: 10.1002/humu.24335 – volume: 14 start-page: 178 year: 2013 ident: 2023010804300289000_B3 article-title: Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration publication-title: Brief. Bioinform. doi: 10.1093/bib/bbs017 – volume: 27 start-page: 2156 year: 2011 ident: 2023010804300289000_B9 article-title: The variant call format and VCFtools publication-title: Bioinforma. Oxf. Engl. doi: 10.1093/bioinformatics/btr330 – volume: 12 start-page: e0170365 year: 2017 ident: 2023010804300289000_B14 article-title: Clinical practice guidelines for rare diseases: the orphanet database publication-title: PLoS One doi: 10.1371/journal.pone.0170365 – volume: 44 start-page: D733 year: 2016 ident: 2023010804300289000_B21 article-title: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkv1189 – volume: 31 start-page: 159 year: 2021 ident: 2023010804300289000_B6 article-title: Accessing NCBI data using the NCBI sequence viewer and genome data viewer (GDV) publication-title: Genome Res. doi: 10.1101/gr.266932.120 – volume: 29 start-page: 308 year: 2001 ident: 2023010804300289000_B16 article-title: dbSNP: the NCBI database of genetic variation publication-title: Nucleic Acids Res. doi: 10.1093/nar/29.1.308 – volume: 562 start-page: 367 year: 2018 ident: 2023010804300289000_B19 article-title: Single-cell transcriptomics of 20 mouse organs creates a tabula muris publication-title: Nature doi: 10.1038/s41586-018-0590-4 – volume: 369 start-page: 1318 year: 2020 ident: 2023010804300289000_B28 article-title: The GTEx consortium atlas of genetic regulatory effects across human tissues publication-title: Science doi: 10.1126/science.aaz1776 – volume: 84 start-page: 524 year: 2009 ident: 2023010804300289000_B13 article-title: DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources publication-title: Am. J. Hum. Genet. doi: 10.1016/j.ajhg.2009.03.010 – volume: 41 start-page: D36 year: 2013 ident: 2023010804300289000_B33 article-title: GenBank publication-title: Nucleic Acids Res. doi: 10.1093/nar/gks1195 – volume: 12 start-page: 996 year: 2002 ident: 2023010804300289000_B1 article-title: The human genome browser at UCSC publication-title: Genome Res. doi: 10.1101/gr.229102 – volume: 12 start-page: 656 year: 2002 ident: 2023010804300289000_B12 article-title: BLAT—The BLAST-Like alignment tool publication-title: Genome Res. – volume: 50 start-page: D1115 year: 2021 ident: 2023010804300289000_B7 article-title: The UCSC genome browser database: 2022 update publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab959 – volume: 53 start-page: 809 year: 2021 ident: 2023010804300289000_B29 article-title: Ultrafast sample placement on existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic publication-title: Nat. Genet. doi: 10.1038/s41588-021-00862-7 – volume: 50 start-page: W774 year: 2022 ident: 2023010804300289000_B4 article-title: WashU epigenome browser update 2022 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkac238 – volume: 38 start-page: 5819 year: 2021 ident: 2023010804300289000_B31 article-title: A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msab264 – year: 2022 ident: 2023010804300289000_B35 article-title: The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution genomics – volume: 26 start-page: 2204 year: 2010 ident: 2023010804300289000_B8 article-title: BigWig and bigbed: enabling browsing of large distributed datasets publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq351 – volume: 24 start-page: 1732 year: 2022 ident: 2023010804300289000_B15 article-title: The gene curation coalition: a global effort to harmonize gene–disease evidence resources publication-title: Genet. Med. doi: 10.1016/j.gim.2022.04.017 – volume: 587 start-page: 246 year: 2020 ident: 2023010804300289000_B25 article-title: Progressive cactus is a multiple-genome aligner for the thousand-genome era publication-title: Nature doi: 10.1038/s41586-020-2871-y – volume: 7 start-page: veab064 year: 2021 ident: 2023010804300289000_B30 article-title: Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool publication-title: Virus Evol. doi: 10.1093/ve/veab064 – volume: 48 start-page: D682 year: 2020 ident: 2023010804300289000_B36 article-title: Ensembl 2020 publication-title: Nucleic Acids Res. – volume: 17 start-page: 66 year: 2016 ident: 2023010804300289000_B5 article-title: JBrowse: a dynamic web platform for genome visualization and analysis publication-title: Genome Biol. doi: 10.1186/s13059-016-0924-1 – volume: 376 start-page: 44 year: 2022 ident: 2023010804300289000_B34 article-title: The complete sequence of a human genome publication-title: Science doi: 10.1126/science.abj6987 – volume: 37 start-page: 4578 year: 2021 ident: 2023010804300289000_B18 article-title: UCSC cell browser: visualize your single-cell data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab503 – volume: 50 start-page: D988 year: 2022 ident: 2023010804300289000_B2 article-title: Ensembl 2022 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab1049
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