title: HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.
abstract: BACKGROUND
  Identification of motifs in biological sequences is a challenging problem because such motifs are often short, degenerate, and may contain gaps. Most algorithms that have been developed for motif-finding use the expectation-maximization (EM) algorithm iteratively. Although EM algorithms can converge quickly, they depend strongly on initialization parameters and can converge to local sub-optimal solutions. In addition, they cannot generate gapped motifs. The effectiveness of EM algorithms in motif finding can be improved by incorporating methods that choose different sets of initial parameters to enable escape from local optima, and that allow gapped alignments within motif models.
  
  
  RESULTS
  We have developed HIGEDA, an algorithm that uses the hierarchical gene-set genetic algorithm (HGA) with EM to initiate and search for the best parameters for the motif model. In addition, HIGEDA can identify gapped motifs using a position weight matrix and dynamic programming to generate an optimal gapped alignment of the motif model with sequences from the dataset. We show that HIGEDA outperforms MEME and other motif-finding algorithms on both DNA and protein sequences.
  
  
  METHODS
  Source code and test datasets are available for download at http://ouray.cudenver.edu/~tnle/, implemented in C++ and supported on Linux and MS Windows.
authors.affiliation: Department of Computer Science and Engineering, Computational Biosciences Program, University of Colorado, Denver, CO, USA.
authors.forename: Thanh
authors.initials: T
authors.lastname: Le
authors.forename: Tom
authors.initials: T
authors.lastname: Altman
authors.forename: Katheleen
authors.initials: K
authors.lastname: Gardiner
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins; D004247:DNA