The UCSC Genome Browser database: extensions and updates 2013

The UCSC Genome Browser database: extensions and updates 2013

2013, Vol. 41, Database issue | Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Brian J. Raney, Andy Pohl, Venkat S. Malladi, Chin H. Li, Brian T. Lee, Katrina Learned, Vanessa Kirkup, Fan Hsu, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Mary Goldman, Belinda M. Giardine, Pauline A. Fujita, Timothy R. Dreszer, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler and W. James Kent
The UCSC Genome Browser (http://genome.ucsc.edu) provides online access to a comprehensive database of genomic sequences and annotations for various organisms. As of September 2012, the browser supports 63 organisms, including 26 mammals, 13 non-mammalian vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast, and sea hares. In the past year, 19 new genome assemblies have been added, with another 28 expected to be released in early 2013. The browser has also seen significant updates to its annotation tracks, including an updated UCSC Genes track for human and mouse assemblies. New features, such as improved navigation menus, have been introduced to enhance usability. The browser now supports multiple sequence alignments, expression, regulation, variation, and phenotype tracks for many assemblies. Additionally, the browser has added a Publications track that links DNA and protein sequences, SNPs, cytogenetic bands, and gene symbols to relevant scientific articles. Software improvements include enhanced VCF support, haplotype sorting display, and the introduction of public track hubs for external data providers. Future plans include adding or updating several annotation tracks, developing tools for integrating diverse annotations with user-provided genomic variants, and implementing a supported mirror in Germany to improve access speed for European users.The UCSC Genome Browser (http://genome.ucsc.edu) provides online access to a comprehensive database of genomic sequences and annotations for various organisms. As of September 2012, the browser supports 63 organisms, including 26 mammals, 13 non-mammalian vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast, and sea hares. In the past year, 19 new genome assemblies have been added, with another 28 expected to be released in early 2013. The browser has also seen significant updates to its annotation tracks, including an updated UCSC Genes track for human and mouse assemblies. New features, such as improved navigation menus, have been introduced to enhance usability. The browser now supports multiple sequence alignments, expression, regulation, variation, and phenotype tracks for many assemblies. Additionally, the browser has added a Publications track that links DNA and protein sequences, SNPs, cytogenetic bands, and gene symbols to relevant scientific articles. Software improvements include enhanced VCF support, haplotype sorting display, and the introduction of public track hubs for external data providers. Future plans include adding or updating several annotation tracks, developing tools for integrating diverse annotations with user-provided genomic variants, and implementing a supported mirror in Germany to improve access speed for European users.
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