ArticleBioinformatics (Oxford, England)2011
Improved similarity scores for comparing motifs.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- RhoC in association with TET2/WDR5 regulates cancer stem cells by epigenetically modifying the expression of pluripotency genes.Cellular and molecular life sciences : CMLS · 2022Article
- Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.Science advances · 2022Article
- Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet.International journal of molecular sciences · 2022Article
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- Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria.Developmental cell · 2020Article
- Ovarian dysfunction following prenatal exposure to an insecticide, chlordecone, associates with altered epigenetic features.Epigenetics & chromatin · 2019Article
- A systematic approach to RNA-associated motif discovery.BMC genomics · 2018Article
- RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.Nucleic acids research · 2017Article
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5 authors.
Funding
Abstract
motivationA question that often comes up after applying a motif finder to a set of co-regulated DNA sequences is whether the reported putative motif is similar to any known motif. While several tools have been designed for this task, Habib et al. pointed out that the scores that are commonly used for measuring similarity between motifs do not distinguish between a good alignment of two informative columns (say, all-A) and one of two uninformative columns. This observation explains why tools such as Tomtom occasionally return an alignment of uninformative columns which is clearly spurious. To address this problem, Habib et al. suggested a new score [Bayesian Likelihood 2-Component (BLiC)] which uses a Bayesian information criterion to penalize matches that are also similar to the background distribution.
resultsWe show that the BLiC score exhibits other, highly undesirable properties, and we offer instead a general approach to adjust any motif similarity score so as to reduce the number of reported spurious alignments of uninformative columns. We implement our method in Tomtom and show that, without significantly compromising Tomtom's retrieval accuracy or its runtime, we can drastically reduce the number of uninformative alignments. AVAILABILITY AND IMPLEMENTATION: The modified Tomtom is available as part of the MEME Suite at http://meme.nbcr.net.
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