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The Human Genome Browser at UCSC
Open accessAbstract
As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu . This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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“To identify specific genes with reduced H3K9me2 levels, we performed H3K9me2-based ChIP-sequencing (ChIP-seq) in biological duplicate (Fig. 4a, http://genome.ucsc.edu30), and validated significantly H3K9me2 depleted genes with quantitative PCR (qPCR) (Fig. 4b).”
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“we have observed that the genomic region distal to the HSA2 fusion site maps well to the near-telomeric region of chimpanzee chromosome 2B, and thus the corresponding UBCS statistics has high values (Fig. 1).”
From Revised time estimation of the ancestral human chromosome 2 fusion (2022) · cites this paper as [29]
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“Hematologic phenotypes of a balanced mix of male and female mice for all models were examined at more than 7 weeks of age to avoid inter-individual variation42.”
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Metadata
- Authors
- Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D.
- Affiliations
- Howard Hughes Medical Institute (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-05-16
- Volume
- 12
- Issue
- 6
- Pages
- 996-1006
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC186604
- OpenAlex
- W2128016314
- Cited by
- 10,400
- References
- 41
- Citations by year
- 2026: 174 · 2025: 366 · 2024: 686 · 2023: 771 · 2022: 765 · 2021: 828 · 2020: 714 · 2019: 677 · 2018: 594 · 2017: 526 · 2016: 530 · 2015: 522 · 2014: 461 · 2013: 449 · 2012: 362
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Genome Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy (FG0399ER62849)
- National Human Genome Research Institute (P41HG002371, 1P41 HG 02371-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- UCSC Genome Browser, expressed sequence tags, gene prediction, cross-species homology, single nucleotide polymorphisms, sequence-tagged sites, MySQL
- MeSH terms
- California, Database Management Systems, Genes, Humans, RNA, Messenger, Sequence Homology, Nucleic Acid, Software, Universities, Gene Expression, Genome, Human, Databases, Genetic
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