The UCSC Genome Browser is a web-based resource that provides a large database of publicly available sequence and annotation data, along with tools for examining and comparing genomes. As of September 2009, genomic sequence and basic annotation tracks were available for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, and a yeast. New data included an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks, and 16 new ENCODE tracks. New features included drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats (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. The UCSC Genome Browser is used by the biomedical community to access sequence and annotations for human and other vertebrate reference species genomes, along with selected model invertebrates. Annotation tracks include assembly and gaps, GC content, RefSeq gene alignments, and repeat region annotations. Comparative genomics tracks show pairwise genomic sequence alignments between organisms. About half of the organisms hosted in the browser include multiple sequence alignment (multiz) tracks. The Genome Browser offers several tools for visualizing and analyzing genome sequences and annotation tracks, including BLAT, in silico PCR, LiftOver, Table Browser, Gene Sorter, Proteome Browser, VisiGene, and custom tracks. The browser is integrated with other tools, and users can access help and training resources. New assemblies included updates for horse, human, opossum, medaka, and yeast. The new human assembly, UCSC version hg19, includes pairwise alignments to 4 primates, 7 non-primate placental mammals, and 12 non-placental vertebrates. The browser also includes new annotation tracks, including the 44-species vertebrate alignment and conservation track, OMIM genes, variation tracks, and expression tracks. New features include drag-and-zoom navigation, the Wiki track for user-added annotations, custom tracks for large datasets, and tools to bridge genomic variation and protein structure. The browser also includes in silico PCR for transcribed sequences and CDS FASTA alignments. Performance enhancements were made to the browser's code and hardware. Future directions include incorporating new assemblies and data from the 1000 Genomes Project, as well as supporting BAM as a custom track file format. Contact information is provided for questions and feedback.The UCSC Genome Browser is a web-based resource that provides a large database of publicly available sequence and annotation data, along with tools for examining and comparing genomes. As of September 2009, genomic sequence and basic annotation tracks were available for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, and a yeast. New data included an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks, and 16 new ENCODE tracks. New features included drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats (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. The UCSC Genome Browser is used by the biomedical community to access sequence and annotations for human and other vertebrate reference species genomes, along with selected model invertebrates. Annotation tracks include assembly and gaps, GC content, RefSeq gene alignments, and repeat region annotations. Comparative genomics tracks show pairwise genomic sequence alignments between organisms. About half of the organisms hosted in the browser include multiple sequence alignment (multiz) tracks. The Genome Browser offers several tools for visualizing and analyzing genome sequences and annotation tracks, including BLAT, in silico PCR, LiftOver, Table Browser, Gene Sorter, Proteome Browser, VisiGene, and custom tracks. The browser is integrated with other tools, and users can access help and training resources. New assemblies included updates for horse, human, opossum, medaka, and yeast. The new human assembly, UCSC version hg19, includes pairwise alignments to 4 primates, 7 non-primate placental mammals, and 12 non-placental vertebrates. The browser also includes new annotation tracks, including the 44-species vertebrate alignment and conservation track, OMIM genes, variation tracks, and expression tracks. New features include drag-and-zoom navigation, the Wiki track for user-added annotations, custom tracks for large datasets, and tools to bridge genomic variation and protein structure. The browser also includes in silico PCR for transcribed sequences and CDS FASTA alignments. Performance enhancements were made to the browser's code and hardware. Future directions include incorporating new assemblies and data from the 1000 Genomes Project, as well as supporting BAM as a custom track file format. Contact information is provided for questions and feedback.