ArticleBioMed research international2015
An Affinity Propagation-Based DNA Motif Discovery Algorithm.
Article in BioMed research international, 2015. 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.
- A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.Entropy (Basel, Switzerland) · 2019Article
- An Entropy-Based Position Projection Algorithm for Motif Discovery.BioMed research international · 2016Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.
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