The UCSC Table Browser data retrieval tool

Donna Karolchik

Angela Hinrichs

Terrence Furey

Krishna Roskin

Charles Sugnet

David Haussler

W Kent

Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), School of Engineering, 1156 High Street, Santa Cruz, CA 95064-1077, USA

^{To whom correspondence should be addressed. Tel: +1 831 459 1544; Fax: +1 831 459 4829; Email:}ude.cscu.eos@kannod

^{The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors}

Received 2003 Aug 15; Revised 2003 Sep 30; Accepted 2003 Oct 13.

Abstract

The University of California Santa Cruz (UCSC) Table Browser (http://genome.ucsc.edu/cgi-bin/hgText) provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database. A flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab- delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks. The Table Browser User’s Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output.

Abstract

ACKNOWLEDGEMENTS

We would like to thank the many collaborators who have contributed sequence and annotation data to our project, as well as our users for their feedback and support. The UCSC Table Browser project is funded by the National Human Genome Research Institute (NHGRI) Grant 1P41HG02371 and the Howard Hughes Medical Institute (HHMI). C.S. is a Howard Hughes Medical Institute Predoctoral Fellow.

ACKNOWLEDGEMENTS

REFERENCES

References

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