The UCSC Genome Browser database: update 2011

The UCSC Genome Browser database: update 2011

2011 | Pauline A. Fujita, Brooke Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, Antonio Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda M. Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler and W. James Kent
The UCSC Genome Browser is an online database providing access to genomic sequence and annotation data for various organisms. It offers tools for visualizing, comparing, and analyzing genomic data, including alignment and uploading user data. New features include a gene search tool, annotation track drag-reorder functionality, and support for BAM and BigWig/BigBed file formats. Display enhancements include transparent coloring for multiple wiggle tracks, a 'mean+whiskers' windowing function, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. Updates to existing tracks are also described. The browser hosts the Data Coordination Center for the ENCODE project and provides tools for retrieving and analyzing genomic data, including the Table Browser, BLAT, and LiftOver utilities. New features include support for external software like GREAT, and the ability to send genomic region data to the Genomic Regions Enrichment of Annotations Tool. New assemblies and tracks for various organisms are also introduced. The browser continues to update and add new data, including variation and medical genomics data. Future directions include incorporating new features, adding new assemblies, and improving data display and extraction capabilities. The browser also provides support for cloud computing and mirror sites. Contact information and funding sources are provided.The UCSC Genome Browser is an online database providing access to genomic sequence and annotation data for various organisms. It offers tools for visualizing, comparing, and analyzing genomic data, including alignment and uploading user data. New features include a gene search tool, annotation track drag-reorder functionality, and support for BAM and BigWig/BigBed file formats. Display enhancements include transparent coloring for multiple wiggle tracks, a 'mean+whiskers' windowing function, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. Updates to existing tracks are also described. The browser hosts the Data Coordination Center for the ENCODE project and provides tools for retrieving and analyzing genomic data, including the Table Browser, BLAT, and LiftOver utilities. New features include support for external software like GREAT, and the ability to send genomic region data to the Genomic Regions Enrichment of Annotations Tool. New assemblies and tracks for various organisms are also introduced. The browser continues to update and add new data, including variation and medical genomics data. Future directions include incorporating new features, adding new assemblies, and improving data display and extraction capabilities. The browser also provides support for cloud computing and mirror sites. Contact information and funding sources are provided.
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