ArticleNucleic acids research2011
STEME: efficient EM to find motifs in large data sets.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Freezing firefly algorithm for efficient planted (ℓ, d) motif search.Medical & biological engineering & computing · 2022Article
- STREME: accurate and versatile sequence motif discovery.Bioinformatics (Oxford, England) · 2021Article
- A noncanonical AR addiction drives enzalutamide resistance in prostate cancer.Nature communications · 2021Article
- ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.Bioinformatics (Oxford, England) · 2019Article
- SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing.Bioinformatics (Oxford, England) · 2019Article
- A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.Entropy (Basel, Switzerland) · 2019Article
- GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- ATF3 negatively regulates cellular antiviral signaling and autophagy in the absence of type I interferons.Scientific reports · 2017Article
- Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites.Current genomics · 2017Review
- Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.Nucleic acids research · 2016Article
- PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets.BioMed research international · 2016Article
- Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets.Bioinformatics (Oxford, England) · 2015Article
- A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets.BioMed research international · 2015Article
- MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures.BMC genomics · 2015Article
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
- EXTREME: an online EM algorithm for motif discovery.Bioinformatics (Oxford, England) · 2014Article
- STEME: a robust, accurate motif finder for large data sets.PloS one · 2014Article
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2 authors.
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Abstract
MEME and many other popular motif finders use the expectation-maximization (EM) algorithm to optimize their parameters. Unfortunately, the running time of EM is linear in the length of the input sequences. This can prohibit its application to data sets of the size commonly generated by high-throughput biological techniques. A suffix tree is a data structure that can efficiently index a set of sequences. We describe an algorithm, Suffix Tree EM for Motif Elicitation (STEME), that approximates EM using suffix trees. To the best of our knowledge, this is the first application of suffix trees to EM. We provide an analysis of the expected running time of the algorithm and demonstrate that STEME runs an order of magnitude more quickly than the implementation of EM used by MEME. We give theoretical bounds for the quality of the approximation and show that, in practice, the approximation has a negligible effect on the outcome. We provide an open source implementation of the algorithm that we hope will be used to speed up existing and future motif search algorithms.
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