The UCSC Genome Browser Database (GBD) provides sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. It includes assembly data, sequence composition, genes, mRNA, expressed sequence tags, comparative genomics, regulation, expression, and variation data. The database is optimized for fast interactive performance with web tools that allow powerful visualization and querying. The Genome Browser displays a wide variety of annotations at all scales, from single nucleotide level to full chromosome. The Table Browser provides direct access to database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD has expanded to include many new species, including chimp, Rhesus macaque, dog, cow, opossum, chicken, frog, fugu, zebrafish, Tetraodon, fruitfly, honeybee, mosquito, sea squirt, and yeast. Genome-wide multi-species alignments and conservation scores are now available for human, mouse, dog, chicken, zebrafish, and fly. The UCSC Known Genes dataset is created by a fully automated process that combines protein and mRNA evidence. The Proteome Browser now includes proteins of all organisms in the UniProt databases. Cross-species protein alignments are useful in newly sequenced genomes that do not yet have well-developed gene annotations. The ENCODE project has added >50 new data tracks to the human browser database. The MGC is a trans-NIH initiative providing full-length open reading frame clones for human, mouse, and rat genes. The CCDS project provides a high-quality, consistently annotated core set of human protein-coding genes. Other new gene annotations include Vega Genes, Vega Pseudogenes, ECgene, Twinscan, SGP, Geneid, Augustus, Yale Pseudogenes, and Superfamily. New expression data include data from the Genomics Institute of the Novartis Research Foundation (GNF) and the Affymetrix Transcriptome Project Phase 2. New variation data include SNPs from dbSNP and commercially available genotyping arrays. New visualization features include 'wiggle' tracks for continuous-valued data, conservation tracks, and chromosome ideograms. New display modes include 'pack' and 'squish' modes. New labeling options in gene annotations, mRNA, and Base Position tracks allow coloring and labeling of amino acids. New PostScript or PDF image generation allows publication-quality images. New table browser interface and functionality include support for queries on related tables, correlation features, and special support for wiggle and multi-species alignment tables. New tools include the Gene Sorter, LiftOver, and In Silico PCR. ProcessThe UCSC Genome Browser Database (GBD) provides sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. It includes assembly data, sequence composition, genes, mRNA, expressed sequence tags, comparative genomics, regulation, expression, and variation data. The database is optimized for fast interactive performance with web tools that allow powerful visualization and querying. The Genome Browser displays a wide variety of annotations at all scales, from single nucleotide level to full chromosome. The Table Browser provides direct access to database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD has expanded to include many new species, including chimp, Rhesus macaque, dog, cow, opossum, chicken, frog, fugu, zebrafish, Tetraodon, fruitfly, honeybee, mosquito, sea squirt, and yeast. Genome-wide multi-species alignments and conservation scores are now available for human, mouse, dog, chicken, zebrafish, and fly. The UCSC Known Genes dataset is created by a fully automated process that combines protein and mRNA evidence. The Proteome Browser now includes proteins of all organisms in the UniProt databases. Cross-species protein alignments are useful in newly sequenced genomes that do not yet have well-developed gene annotations. The ENCODE project has added >50 new data tracks to the human browser database. The MGC is a trans-NIH initiative providing full-length open reading frame clones for human, mouse, and rat genes. The CCDS project provides a high-quality, consistently annotated core set of human protein-coding genes. Other new gene annotations include Vega Genes, Vega Pseudogenes, ECgene, Twinscan, SGP, Geneid, Augustus, Yale Pseudogenes, and Superfamily. New expression data include data from the Genomics Institute of the Novartis Research Foundation (GNF) and the Affymetrix Transcriptome Project Phase 2. New variation data include SNPs from dbSNP and commercially available genotyping arrays. New visualization features include 'wiggle' tracks for continuous-valued data, conservation tracks, and chromosome ideograms. New display modes include 'pack' and 'squish' modes. New labeling options in gene annotations, mRNA, and Base Position tracks allow coloring and labeling of amino acids. New PostScript or PDF image generation allows publication-quality images. New table browser interface and functionality include support for queries on related tables, correlation features, and special support for wiggle and multi-species alignment tables. New tools include the Gene Sorter, LiftOver, and In Silico PCR. Process