chapter  9
28 Pages

◾ Dynamic Annotation Systems: End-User-Driven Annotation and Visualization

Over the years, the UCSC Genome Browser database (Dreszer et al., 2012) has been expanded to provide access to genome annotations from many external sources as well as from UCSC. Updates on the database in terms of new genome assemblies and annotations are provided annually on the Database issue of the journal Nucleic Acids Research (http://nar. oxfordjournals.org). ™ese sequences and annotations have been generated from a variety of sources, including the UCSC annotation pipeline and collaborators from research centers worldwide. UCSC manages the oªcial repository of sequence-related data for the Encyclopedia of DNA Elements (ENCODE) consortium (http://genome.ucsc.edu/ENCODE) (ENCODE Consortium, 2004; Rosenbloom et al., 2012) and supports the coordination of data submission, storage, retrieval, and visualization. ENCODE started in September 2003 with the goal of identifying functional elements in the human genome sequence.