ArticleBioinformatics (Oxford, England)2012
Large-scale motif discovery using DNA Gray code and equiprobable oligomers.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data.Scientific reports · 2017Article
- PISMA: A Visual Representation of Motif Distribution in DNA Sequences.Bioinformatics and biology insights · 2017Article
- Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets.Bioinformatics (Oxford, England) · 2015Article
- Article
- A dictionary based informational genome analysis.BMC genomics · 2012Article
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3 authors.
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Abstract
motivationHow to find motifs from genome-scale functional sequences, such as all the promoters in a genome, is a challenging problem. Word-based methods count the occurrences of oligomers to detect excessively represented ones. This approach is known to be fast and accurate compared with other methods. However, two problems have hampered the application of such methods to large-scale data. One is the computational cost necessary for clustering similar oligomers, and the other is the bias in the frequency of fixed-length oligomers, which complicates the detection of significant words.
resultsWe introduce a method that uses a DNA Gray code and equiprobable oligomers, which solve the clustering problem and the oligomer bias, respectively. Our method can analyze 18 000 sequences of ~1 kbp long in 30 s. We also show that the accuracy of our method is superior to that of a leading method, especially for large-scale data and small fractions of motif-containing sequences. AVAILABILITY: The online and stand-alone versions of the application, named Hegma, are available at our website: http://www.genome.ist.i.kyoto-u.ac.jp/~ichinose/hegma/ CONTACT: ichinose@i.kyoto-u.ac.jp; o.gotoh@i.kyoto-u.ac.jp
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