ArticleBMC bioinformatics2018
A new sequence logo plot to highlight enrichment and depletion.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis.bioRxiv : the preprint server for biology · 2023Article
- Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT.Cell · 2022Article
- Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors.BMC bioinformatics · 2022Article
- Generalizable strategy to analyze domains in the context of parent protein architecture: A CheW case study.Proteins · 2022Article
- Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine.Molecular cell · 2022Article
- Adaptation by Type V-A and V-B CRISPR-Cas Systems Demonstrates Conserved Protospacer Selection Mechanisms Between Diverse CRISPR-Cas Types.The CRISPR journal · 2022Article
- Cellular and genetic drivers of RNA editing variation in the human brain.Nature communications · 2022Article
- Computational analysis and prediction of PE_PGRS proteins using machine learning.Computational and structural biotechnology journal · 2022Article
- ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides.Briefings in bioinformatics · 2021Article
- Article
- Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples.Nature communications · 2021Article
- Inhibition of Syk promotes chemical reprogramming of fibroblasts via metabolic rewiring and HThe EMBO journal · 2021Article
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundSequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail to highlight interesting depletions. Current alternatives that try to highlight depletion often produce visually cluttered logos.
resultsWe introduce a new sequence logo plot, the EDLogo plot, that highlights both enrichment and depletion, while minimizing visual clutter. We provide an easy-to-use and highly customizable R package Logolas to produce a range of logo plots, including EDLogo plots. This software also allows elements in the logo plot to be strings of characters, rather than a single character, extending the range of applications beyond the usual DNA, RNA or protein sequences. And the software includes new Empirical Bayes methods to stabilize estimates of enrichment and depletion, and thus better highlight the most significant patterns in data. We illustrate our methods and software on applications to transcription factor binding site motifs, protein sequence alignments and cancer mutation signature profiles.
conclusionsOur new EDLogo plots and flexible software implementation can help data analysts visualize both enrichment and depletion of characters (DNA sequence bases, amino acids, etc.) across a wide range of applications.
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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.