UCSC Genome Browser
UCSC Genome Browser provides integrated visualization, integration, and analysis of genomic sequence and annotation data across multiple organisms to support comparative genomics, variant interpretation, and regulatory and transcriptomic analyses.
Key Features:
- Comprehensive Data Coverage: Hosts genomic assemblies and annotation tracks for over 60 genomes, including human (hg38/GRCh38), bonobo, zebrafish, orangutan, and marmoset.
- Integrated Tool Set: Includes BLAT for rapid sequence alignment, the Table Browser for complex genome-wide queries, and the Gene Sorter for filtering genes by various metrics.
- Visualization of Diverse Data Types: Presents mRNA mappings, gene predictions, regulatory elements, expression data, SNPs, repeats, and other annotation tracks.
- Data Integration and File Format Support: Supports BAM, CRAM, BigWig, and BigBed formats and provides the Data Integrator for intersecting data across multiple tracks and linking to external databases.
- Community Annotations and User Data: Supports a Wiki track for user-contributed annotations and the upload of user datasets and custom annotation tracks.
- Specialized Tools and Track Types: Provides the Proteome Browser, VisiGene, Genome Graphs, ChIP-Seq peak tracks, and long-range chromatin interaction pair tracks.
- Continuous Updates and Clinical Resources: Incorporates new genome assemblies and annotation sets and integrates phenotype-associated and disease-related variant information from sources such as ClinVar and ClinGen.
Scientific Applications:
- Comparative Genomics: Enables cross-species and cross-assembly genome comparisons for evolutionary and comparative analyses.
- Sequence Alignment and Mapping: Supports rapid sequence alignment and mapping with BLAT and alignment file formats (BAM/CRAM).
- Variant Interpretation and Clinical Annotation: Integrates phenotype-associated and disease-related variants with ClinVar and ClinGen links to support variant interpretation.
- Regulatory Genomics and Chromatin Structure: Facilitates analysis of regulatory elements, ChIP-Seq peak data, and long-range chromatin interactions.
- Transcriptomics and Gene Expression: Maps mRNA and expression data to genome assemblies to support transcript annotation and expression analyses.
- Protein and Gene-Centric Analyses: Enables protein property visualization and gene-centric exploration via the Proteome Browser and VisiGene.
- Data Extraction and Cross-Track Analyses: Allows complex dataset extraction and intersection across tracks using the Table Browser and Data Integrator.
Methodology:
Sequence alignment with BLAT; genome-wide queries via the Table Browser; gene filtering with Gene Sorter; track intersection via the Data Integrator; support for BAM, CRAM, BigWig, and BigBed formats; and specialized track types including ChIP-Seq peak displays and long-range chromatin interaction pairs.
Topics
Collections
Details
- License:
- Apache-2.0
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 3/27/2017
- Last Updated:
- 11/24/2024
Operations
Publications
Karolchik D. The UCSC Genome Browser Database. Nucleic Acids Research. 2003;31(1):51-54. doi:10.1093/nar/gkg129. PMID:12519945. PMCID:PMC165576.
Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Research. 2009;37(Database):D755-D761. doi:10.1093/nar/gkn875. PMID:18996895. PMCID:PMC2686463.
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research. 2013;42(D1):D764-D770. doi:10.1093/nar/gkt1168. PMID:24270787. PMCID:PMC3964947.
Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Research. 2009;38(Database):D613-D619. doi:10.1093/nar/gkp939. PMID:19906737. PMCID:PMC2808870.
Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Research. 2011;40(D1):D912-D917. doi:10.1093/nar/gkr1012. PMID:22075998. PMCID:PMC3245183.
Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, James Kent W. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research. 2011;40(D1):D918-D923. doi:10.1093/nar/gkr1055. PMID:22086951. PMCID:PMC3245018.
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler aD. The Human Genome Browser at UCSC. Genome Research. 2002;12(6):996-1006. doi:10.1101/gr.229102. PMID:12045153. PMCID:PMC186604.
Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research. 2007;36(Database):D773-D779. doi:10.1093/nar/gkm966. PMID:18086701. PMCID:PMC2238835.
Hinrichs AS. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 2006;34(90001):D590-D598. doi:10.1093/nar/gkj144. PMID:16381938. PMCID:PMC1347506.
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AFA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 2014;43(D1):D670-D681. doi:10.1093/nar/gku1177. PMID:25428374. PMCID:PMC4383971.
Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2016 update. Nucleic Acids Research. 2015;44(D1):D717-D725. doi:10.1093/nar/gkv1275. PMID:26590259. PMCID:PMC4702902.
Unknown Authors. OUP accepted manuscript. Nucleic Acids Research. 2016. doi:10.1093/nar/gkw1134. PMID:27899642. PMCID:PMC5210591.
Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2019 update. Nucleic Acids Research. 2018;47(D1):D853-D858. doi:10.1093/nar/gky1095. PMID:30407534. PMCID:PMC6323953.
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Research. 2012;41(D1):D64-D69. doi:10.1093/nar/gks1048. PMID:23155063. PMCID:PMC3531082.
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Research. 2010;39(Database):D876-D882. doi:10.1093/nar/gkq963. PMID:20959295. PMCID:PMC3242726.