SPACER

The software tool SPACER is a semi-greedy algorithm used to identify highly degenerate motifs in transcription factors. The algorithm is implemented in Java 1.4 and is freely available for download. SPACER is compared against ten other motif finders on 42 experimentally defined regulons from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae, and its effectiveness in identifying gapped and highly degenerate motifs is demonstrated.

Topic

Protein binding sites;Small molecules;Nucleic acid sites, features and motifs;DNA binding sites;Molecular dynamics

Detail

  • Operation: Peak calling;Protein binding site prediction;Molecular docking;Protein-nucleic acid binding site analysis

  • Software interface: Web user interface

  • Language: Java;C++;C

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Science Foundation

  • Input: -

  • Output: -

  • Contact: Alexandr.Goncearenco@nih.gov;igorb@bii.a-star.edu.sg

  • Collection: -

  • Maturity: -

Publications

  • SPACER: identification of cis-regulatory elements with non-contiguous critical residues.
  • Chakravarty A, et al. SPACER: identification of cis-regulatory elements with non-contiguous critical residues. SPACER: identification of cis-regulatory elements with non-contiguous critical residues. 2007; 23:1029-31. doi: 10.1093/bioinformatics/btm041
  • https://doi.org/10.1093/bioinformatics/btm041
  • PMID: 17470480
  • PMC: -

Download and documentation

    Currently not available or not maintained.

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