ArticleNucleic acids research2012
Efficient motif search in ranked lists and applications to variable gap motifs.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 25 citations in OpenAlex.
- Inferring single-cell and spatial microRNA activity from transcriptomics data.Communications biology · 2025Article
- A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.Nature communications · 2022Article
- Molecular harvesting with electroporation for tissue profiling.Scientific reports · 2019Article
- Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks.Nucleic acids research · 2017Article
- A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications.Nucleic acids research · 2016Article
- RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.Nucleic acids research · 2015Article
- MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures.BMC genomics · 2015Article
- High-throughput characterization of protein-RNA interactions.Briefings in functional genomics · 2015Review
- Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs.Algorithms for molecular biology : AMB · 2014Article
- New strategies for evaluation and analysis of SELEX experiments.BioMed research international · 2014Article
- The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability.Nucleic acids research · 2013Article
- DRIMust: a web server for discovering rank imbalanced motifs using suffix trees.Nucleic acids research · 2013Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence elements, at all levels-DNA, RNA and protein, play a central role in mediating molecular recognition and thereby molecular regulation and signaling. Studies that focus on -measuring and investigating sequence-based recognition make use of statistical and computational tools, including approaches to searching sequence motifs. State-of-the-art motif searching tools are limited in their coverage and ability to address large motif spaces. We develop and present statistical and algorithmic approaches that take as input ranked lists of sequences and return significant motifs. The efficiency of our approach, based on suffix trees, allows searches over motif spaces that are not covered by existing tools. This includes searching variable gap motifs-two half sites with a flexible length gap in between-and searching long motifs over large alphabets. We used our approach to analyze several high-throughput measurement data sets and report some validation results as well as novel suggested motifs and motif refinements. We suggest a refinement of the known estrogen receptor 1 motif in humans, where we observe gaps other than three nucleotides that also serve as significant recognition sites, as well as a variable length motif related to potential tyrosine phosphorylation.
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