The UCSC Genome Browser database: update 2010

By B. Rhead, Donna Karolchik, Robert M. Kuhn, A. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney and 13 more. Nucleic Acids Res., 2009

1,401 citations recorded by the source corpus.

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data. As of September 2009, genomic sequence and a basic set of annotation ‘tracks’ are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.

Subfields: Molecular Biology

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Citations in the corpus

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations (2012, methodology): “…(r) for each position containing laboratory-induced mutations by using the approach of Kumar et al. (2009b) where evolutionary rate is calculated using the appropriate protein sequence alignment from the UCSC Genome Browser (Rhead et al., 2010) and a timetree of 46 species (Kumar and Hedges, 2011).”
Ensembl’s 10th year (2009, positive): “Ensembl, in partnership with NCBI, UCSC and the Havana project, continues to play an active role in the CCDS consortium (9).”
dbNSFP: A Lightweight Database of Human Non-synonymous SNPs and Their Functional Predictions (2011, methodology): “The PhyloP scores were extracted from the placental subset of the precomputed phyloP44way scores [Pollard et al., 2010] provided by the UCSC Genome Browser (see details at http://hgdownload. cse.ucsc.edu/goldenPath/hg18/phyloP44way/).”
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ (2010, positive): “Gene, noncoding RNA, and PhastCons conserved element annotations were obtained from the UCSC genome browser’s [20,21] Known Genes [22], RNA Genes, and Conservation [4] tracks respectively.”
Anchored hybrid enrichment for massively high-throughput phylogenomics. (2012, methodology): “We downloaded genomes of the model species from the UCSC Genome Browser website (genome.ucsc.edu, Fujita et al. 2011): Homo (hg19, February 2009, Human Genome Consortium, 2001), Gallus (galGal3, May 2006), Anolis (anoCar1, February 2007), Xenopus (xenTro2, August 2005), and Danio (danRer6, December…”
Fast Computation and Applications of Genome Mappability (2012, methodology): “mismatches, and a very good approximation of it if a non-zero number of mismatches is allowed. For different number of substitutions, we then examine the genome-wide mappability profiles of four model organisms (human, mouse, fly and nematode), for which we also produced visualization schemes as par”
F-SNP: computationally predicted functional SNPs for disease association studies (2007, methodology): “Conserved region GoldenPath (17) http://genome.”
miRmap: Comprehensive prediction of microRNA target repression strength (2012, positive): “We identified potential miRNA target sites by searching for matches to canonical 7-mer seeds on the transcripts involved in each experiment and predicted their strength with the 11 methods implemented in our miRmap library, and an additional feature derived from the PhastCons UCSC track (see ‘Materi”