title: EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences.
abstract: BACKGROUND
  Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.
  
  
  RESULTS
  We proposed a novel clustering-based ensemble algorithm named EMD for de novo motif discovery by combining multiple predictions from multiple runs of one or more base component algorithms. The ensemble approach is applied to the motif discovery problem for the first time. The algorithm is tested on a benchmark dataset generated from E. coli RegulonDB. The EMD algorithm has achieved 22.4% improvement in terms of the nucleotide level prediction accuracy over the best stand-alone component algorithm. The advantage of the EMD algorithm is more significant for shorter input sequences, but most importantly, it always outperforms or at least stays at the same performance level of the stand-alone component algorithms even for longer sequences.
  
  
  CONCLUSIONS
  We proposed an ensemble approach for the motif discovery problem by taking advantage of the availability of a large number of motif discovery programs. We have shown that the ensemble approach is an effective strategy for improving both sensitivity and specificity, thus the accuracy of the prediction. The advantage of the EMD algorithm is its flexibility in the sense that a new powerful algorithm can be easily added to the system.
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA. hu5@purdue.edu
authors.forename: Jianjun
authors.initials: J
authors.lastname: Hu
authors.forename: Yifeng D
authors.initials: YD
authors.lastname: Yang
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004926:Escherichia coli / Q000378:metabolism; D020869:Gene Expression Profiling; D010363:Pattern Recognition, Automated; D010802:Phylogeny; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D004247:DNA