The UCSC Genome Browser Database: 2008 update

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year’s additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/. INTRODUCTION Fundamental to expanding our knowledge of how the human body works in health and in disease is the capability to access and share data produced through experimentation and computational analysis. The University of California, Santa Cruz (UCSC) Genome Browser Database (GBD) (http://genome.ucsc.edu) (1) provides a common repository for genomic annotation data—including comparative genomics, genes and gene predictions; mRNA and EST alignments; and expression, regulation, variation and assembly data—and robust, flexible tools for viewing, comparing, distributing and analyzing the information. Produced and maintained by the Genome Bioinformatics Group at the UCSC Center for Biomolecular Science and Engineering, the GBD focuses primarily on vertebrate and model organism genomes, with an emphasis on comparative genomics analysis. As of September 2007 the GBD contains data for 11 mammalian species including human, mouse, rat, chimpanzee, rhesus macaque, horse, cow, cat, dog, opossum and platypus; 8 other vertebrates: chicken, lizard (Anolis carolinensis), frog (Xenopus tropicalis), zebrafish, fugu, tetraodon, medaka and stickleback; and 21 invertebrates including 11 flies, honeybee, Anopheles mosquito, five worms, one yeast (Saccharomyces cerevisiae) and two deuterostomes—purple sea urchin and sea squirt. For many of the organisms, more than one assembly is provided, and several older archived assemblies may be *To whom correspondence should be addressed. Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: [email protected]