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Bioinformatics 2007 23(8):1029-1031; doi:10.1093/bioinformatics/btm041
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SPACER: identification of cis-regulatory elements with non-contiguous critical residues

Arijit Chakravarty 1, Jonathan M. Carlson 2, Radhika S. Khetani 3, Charles E. DeZiel 3 and Robert H. Gross 3,*

1Department of Cancer Pharmacology, Millennium Pharmaceuticals Inc., Cambridge, MA, 2Department of Computer Science and Engineering, University of Washington, Seattle, WA and 3Department of Biology, Dartmouth College, Hanover, NH, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Many transcription factors bind to sites that are long and loosely related to each other. De novo identification of such motifs is computationally challenging. In this article, we propose a novel semi-greedy algorithm over the space of all IUPAC degenerate strings to identify the most over-represented highly degenerate motifs.

Results: We present an implementation of this algorithm, named SPACER (Separated Pattern-based Algorithm for cis-Element Recognition) and demonstrate its effectiveness in identifying ‘gapped’ and highly degenerate motifs. We compare SPACER's performance against ten motif finders on 42 experimentally defined regulons from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae. These motif finders cover a wide range of both enumerative and statistical approaches, including programs specifically designed for prokaryotic and ‘gapped’ motifs.

Availability: A Java 1.4 implementation is freely available on the Web at http://genie.Dartmouth.edu/SPACER/

Contact: robert.h.gross{at}dartmouth.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on November 12, 2006; revised on January 31, 2007; accepted on February 1, 2007

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