full-text:
The UCSC Genome Browser database: extensions and updates 2013

The UCSC Genome Browser database: extensions and updates 2013

1. Laurence R. Meyer¹,
2. Ann S. Zweig¹,*,
3. Angie S. Hinrichs¹,
4. Donna Karolchik¹,
5. Robert M. Kuhn¹,
6. Matthew Wong¹,
7. Cricket A. Sloan¹,
8. Kate R. Rosenbloom¹,
9. Greg Roe¹,
10. Brooke Rhead¹,
11. Brian J. Raney¹,
12. Andy Pohl¹,²,
13. Venkat S. Malladi¹,
14. Chin H. Li¹,
15. Brian T. Lee¹,
16. Katrina Learned¹,
17. Vanessa Kirkup¹,
18. Fan Hsu¹,
19. Steve Heitner¹,
20. Rachel A. Harte¹,
21. Maximilian Haeussler¹,
22. Luvina Guruvadoo¹,
23. Mary Goldman¹,
24. Belinda M. Giardine³,
25. Pauline A. Fujita¹,
26. Timothy R. Dreszer¹,
27. Mark Diekhans¹,
28. Melissa S. Cline¹,
29. Hiram Clawson¹,
30. Galt P. Barber¹,
31. David Haussler¹,⁴ and
32. W. James Kent¹

+ Author Affiliations

1. ¹Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, ²Centre for Genomic Regulation (CRG), C/ Dr. Aiguader, 88, 08003 Barcelona, Spain, ³Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 and ⁴Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA

1. ↵*To whom correspondence should be addressed. Tel: +1 831 459 4937; Fax: +1 831 459 1809; Email: ann@soe.ucsc.edu

• Received September 19, 2012.
• Accepted October 8, 2012.

Next Section

Abstract

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation ‘tracks’ are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.