ArticleBioinformatics (Oxford, England)2014
Stochastic EM-based TFBS motif discovery with MITSU.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors.Nucleic acids research · 2019Article
- Direct AUC optimization of regulatory motifs.Bioinformatics (Oxford, England) · 2017Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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3 authors.
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Abstract
motivationThe Expectation-Maximization (EM) algorithm has been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery and underlies the most widely used motif discovery algorithms. In the wider field of probabilistic modelling, the stochastic EM (sEM) algorithm has been used to overcome some of the limitations of the EM algorithm; however, the application of sEM to motif discovery has not been fully explored.
resultsWe present MITSU (Motif discovery by ITerative Sampling and Updating), a novel algorithm for motif discovery, which combines sEM with an improved approximation to the likelihood function, which is unconstrained with regard to the distribution of motif occurrences within the input dataset. The algorithm is evaluated quantitatively on realistic synthetic data and several collections of characterized prokaryotic TFBS motifs and shown to outperform EM and an alternative sEM-based algorithm, particularly in terms of site-level positive predictive value. AVAILABILITY AND IMPLEMENTATION: Java executable available for download at http://www.sourceforge.net/p/mitsu-motif/, supported on Linux/OS X.
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