The UCSC Genome Browser
By Donna Karolchik, A. Hinrichs, W. James Kent. Current Protocols in Human Genetics, 2003
537 citations recorded by the source corpus.
The UCSC Genome Browser 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 ‐ some of which are generated at the University of California, Santa Cruz (UCSC) and some by external collaborators ‐ display gene predictions, mRNA alignments, expressed sequence tag alignments, cross‐species homologies, single nucleotide polymorphisms, and several other types of data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. Users can also upload custom annotation tracks for research or educational use. This unit describes how to use and customize the UCSC Genome Browser, download the underlying database tables, and create and display custom annotation tracks.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/a0cdededbe99cb3be5b65225f2b917867208dce9
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In Molecular Biology
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Citations in the corpus
- The NHGRI GWAS Catalog, a curated resource of SNP-trait associations (2013, methodology): “(iii) GWAS Catalog data are available through commonly used data portals such as Ensembl (17), UCSC Genome Browser (18) and PheGenI (19) and many other community tools.”
- De novo transcriptome assembly with ABySS (2009, unknown): “We aligned these bubble sequences to hg18 using BLAT, requiring 95% or better identity.”
- PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals (2011, methodology): “PoPoolation provides several options to retrieve polymorphism data for specific genomic regions of interest and allows this data to be displayed in FlyBase and the UCSC Genome Browser, thus linking polymorphism data with functional information.”
- Robust Demographic Inference from Genomic and SNP Data (2013, methodology): “We thus considered autosomal SNPs found outside genic regions (as defined by Ensembl version 71, April 2013 [85], and outside CpG islands (as defined on the UCSC platform, [86]).”
- The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools (2014, methodology): “The mechanism used for this purpose is analogous to the batch coordinate conversion method implemented in the liftOver program from the UCSC genome browser (3).”