The UCSC Genome Browser database: update 2010

Abstract

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.

Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution

“…All genomic data were extracted from the UCSC Genome Browser tables (http://genome.ucsc.edu) 48 . Mouse assembly was from July 2007 (mm9), human and chimpanzee from March 2006 (hg18 and panTro2, respectively).…”

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

“…We therefore retrieved all repetitive DNA tracks from the UCSC genome browser 26 and designed filters for each of them (Supplementary Note 2). In addition, we optimized a filter for homopolymer stretches.…”

“…All data from these validation experiments in the tumors (that is, confirmed somatic variants, false-positive and false-negative variants) are accessible in Supplementary Table 1. Functional annotation of SNVs. Several computational tools and databases were used to predict the functional effect of coding and noncoding SNVs, including known or predicted protein coding genes, miRNAs and their target sites 26 , TRANSFAC transcription factor binding sites 44 , OregANNO annotated regulatory sites 45 , Vista Enhancer sites 46 , conservation as indicated by the presence of GERP constraint elements 17 , phastcons conserved elements 47 and repeat elements. The effect of coding mutations was assessed using SIFT 48 , PolyPhen 49 and CanPredict 50 .…”

Application of a systems approach to study developmental gene regulation

“…Visualization and analysis of biological networks can be performed in Cytoscape (Shannon et al 2003). Visualization of genomic datasets can be performed in various public genome browsers, including UCSC Genome Browser (Rhead et al 2010) and IGV (Thorvaldsdóttir et al 2012). For alignment of short sequence reads, one can use Bowtie (Langmead et al 2009).…”