ArticleNucleic acids research2021
Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.
Article in Nucleic acids research, 2021. 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, 12 citations in OpenAlex.
- Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome.Nucleic acids research · 2025Article
- Transcription factor binding site orientation and order are major drivers of gene regulatory activity.Nature communications · 2023Article
- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Surveying mutation density patterns around specific genomic features.Genome research · 2022Article
- Tandem repeats ubiquitously flank and contribute to translation initiation sites.BMC genomic data · 2022Article
- Alternative splicing modulation by G-quadruplexes.Nature communications · 2022Article
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and transcription factor binding. As such, DNA strand asymmetries and mutational strand bias can provide information about biological function. However, a versatile tool to explore this does not exist. Here, we present Asymmetron, a user-friendly computational tool that performs statistical analysis and visualizations for the evaluation of strand asymmetries. Asymmetron takes as input DNA features provided with strand annotation and outputs strand asymmetries for consecutive occurrences of a single DNA feature or between pairs of features. We illustrate the use of Asymmetron by identifying transcriptional and replicative strand asymmetries of germline structural variant breakpoints. We also show that the orientation of the binding sites of 45% of human transcription factors analyzed have a significant DNA strand bias in transcribed regions, that is also corroborated in ChIP-seq analyses, and is likely associated with transcription. In summary, we provide a novel tool to assess DNA strand asymmetries and show how it can be used to derive new insights across a variety of biological disciplines.
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Registered trials
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