Nucleic Acids Research Advance Access originally published online on May 7, 2007
Nucleic Acids Research 2007 35(Web Server issue):W259-W264; doi:10.1093/nar/gkm310
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W259-W264
© 2007 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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SCOPE: a web server for practical de novo motif discovery
1Department of Computer Science and Engineering, University of Washington, Seattle, WA, 2Department of Cancer Pharmacology, Millennium Pharmaceuticals Inc., Cambridge, MA and 3Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
*To whom correspondence should be addressed. Tel: +603 646 2059; Fax: +603 646 1347; Email: robert.h.gross{at}dartmouth.edu
Received January 31, 2007. Revised March 31, 2007. Accepted April 14, 2007.
SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at <http://genie.dartmouth.edu/scope>.
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