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

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  1. Comin, Matteo; Verzotto, Davide: Filtering degenerate patterns with application to protein sequence analysis (2013)
  2. Chakravarty, Arijit; Carlson, Jonathan M.; Khetani, Radhika S.; Deziel, Charles E.; Gross, Robert H.: Spacer: Identification of (c)is-regulatory elements with non-contiguous critical residues (2007) ioport