ArticleBioinformatics (Oxford, England)2021
STREME: accurate and versatile sequence motif discovery.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 390 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
390 citing papers in PubMed.
- Deep learning-drivenSynthetic and systems biotechnology · 2027Article
- Article
- DND1-NANOS3 shapes the PGC transcriptome via a heptanucleotide sequence in mRNA 3' UTRs.Molecular cell · 2026Article
- Multimodal single cell analysis reveals a link between flowering and leaf initiation.bioRxiv : the preprint server for biology · 2026Article
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- Dynamic and non-additive gene regulation shapes maize responses to simultaneous salt and cold stress.Functional & integrative genomics · 2026Article
- TIF1γ regulates stability of regulatory T cells during inflammation.Nature immunology · 2026Article
- Article
- Tailless terminates the neural stem cell temporal cascade in both the optic lobe and central brain.Development (Cambridge, England) · 2026Article
- Regulatory logic of neuronal differentiation in theProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mechanistic basis of LolDF-mediated lipoprotein transport in Acinetobacter.Nature communications · 2026Article
- Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.Genome research · 2026Article
- Asymmetric chromatin accessibility underlies anterior-posterior axis specification in moth fly embryos.PLoS biology · 2026Article
- EvoSNR-Prom: Predicting promoters at single-nucleotide resolution with label-aware transfer learning of the pretrained EVO model.PLoS computational biology · 2026Article
- Honeydew: A Fluorescent Aptamer for Low-Cost Azo Food Dyes.Chembiochem : a European journal of chemical biology · 2026Article
- Hac1-independent functions of Ire1 drive morphogenesis in Candida albicans through distinct transcriptional programs.Journal of cell science · 2026Article
- Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.HGG advances · 2026Article
- Mapping of CELF1-RNA interactions reveals post-transcriptional control of lens development.NAR molecular medicine · 2026Article
- Targeting thymine DNA glycosylase induces synthetic lethality in p53-deficient cancers.Nature chemical biology · 2026Article
- Alternative Polyadenylation Dynamics During the Rice Blast Immune Response.Molecular plant pathology · 2026Article
330 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
motivationSequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences-for example, the binding site motifs of DNA- and RNA-binding proteins.
resultsThe STREME algorithm presented here advances the state-of-the-art in ab initio motif discovery in terms of both accuracy and versatility. Using in vivo DNA (ChIP-seq) and RNA (CLIP-seq) data, and validating motifs with reference motifs derived from in vitro data, we show that STREME is more accurate, sensitive and thorough than several widely used algorithms (DREME, HOMER, MEME, Peak-motifs) and two other representative algorithms (ProSampler and Weeder). STREME's capabilities include the ability to find motifs in datasets with hundreds of thousands of sequences, to find both short and long motifs (from 3 to 30 positions), to perform differential motif discovery in pairs of sequence datasets, and to find motifs in sequences over virtually any alphabet (DNA, RNA, protein and user-defined alphabets). Unlike most motif discovery algorithms, STREME reports a useful estimate of the statistical significance of each motif it discovers. STREME is easy to use individually via its web server or via the command line, and is completely integrated with the widely used MEME Suite of sequence analysis tools. The name STREME stands for 'Simple, Thorough, Rapid, Enriched Motif Elicitation'. AVAILABILITY AND IMPLEMENTATION: The STREME web server and source code are provided freely for non-commercial use at http://meme-suite.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.