title: DECOD: fast and accurate discriminative DNA motif finding.
abstract: BACKGROUND
  Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions.
  
  
  RESULTS
  To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outperforms previous methods both in speed and in accuracy when using simulated and real biological benchmark data. We performed new binding experiments for p53 mutants and used DECOD to identify p53 co-factors, suggesting new mechanisms for p53 activation.
  
  
  BACKGROUND
  The source code and binaries for DECOD are available at http://www.sb.cs.cmu.edu/DECOD CONTACT: zivbj@cs.cmu.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Huggins
authors.forename: Shan
authors.initials: S
authors.lastname: Zhong
authors.forename: Idit
authors.initials: I
authors.lastname: Shiff
authors.forename: Rachel
authors.initials: R
authors.lastname: Beckerman
authors.forename: Oleg
authors.initials: O
authors.lastname: Laptenko
authors.forename: Carol
authors.initials: C
authors.lastname: Prives
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.forename: Itamar
authors.initials: I
authors.lastname: Simon
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D059372:Nucleotide Motifs; D017422:Sequence Analysis, DNA; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D016159:Tumor Suppressor Protein p53; D004247:DNA