Nucleic Acids Research Advance Access originally published online on December 13, 2006
Nucleic Acids Research 2007 35(Database issue):D663-D667; doi:10.1093/nar/gkl1017
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Nucleic Acids Research, 2007, Vol. 35, Database issue D663-D667
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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The ENCODE Project at UC Santa Cruz
1 Department of Biomolecular Engineering, University of California at Santa Cruz Santa Cruz, CA 95064, USA 2 Center for Biomolecular Science and Engineering Santa Cruz, CA 95064, USA 3 Howard Hughes Medical Institute and University of California at Santa Cruz Santa Cruz, CA 95064, USA
*To whom correspondence should be addressed at Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Engineering 2, Suite 501, Mail Stop CBSE/ITI, Santa Cruz, CA 95064, USA Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: daryl{at}soe.ucsc.edu
Received August 15, 2006. Revised November 1, 2006. Accepted November 2, 2006.
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase I hypersensitivity, chromatin immunoprecipitation, promoter function, gene structure, pseudogenes, non-protein-coding RNAs, transcribed RNAs, multiple sequence alignment and evolutionarily constrained elements. The ENCODE project at UCSC website (http://genome.ucsc.edu/ENCODE) is the primary portal for the sequence-based data produced as part of the ENCODE project. In the pilot phase of the project, over 30 labs provided experimental results for a total of 56 browser tracks supported by 385 database tables. The site provides researchers with a number of tools that allow them to visualize and analyze the data as well as download data for local analyses. This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project. Access to the data and types of interactive analysis that are possible are illustrated through supplemental examples.
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