Document Type

Article

Publication Date

4-14-2007

Publication Title

Nucleic Acids Research

Department

Department of Biological Sciences

Abstract

SCOPE is a novel parameter-free method for the de novoidentification 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>.

DOI

10.1093/nar/gkm310

Original Citation

Carlson JM, Chakravarty A, DeZiel CE, Gross RH. SCOPE: a web server for practical de novo motif discovery. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W259-64. doi: 10.1093/nar/gkm310. Epub 2007 May 7. PMID: 17485471; PMCID: PMC1933170.

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