ArticleNucleic acids research2013
Categorical spectral analysis of periodicity in human and viral genomes.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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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.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Distinct YY dinucleotide periodicity in adeno-associated virus DNA.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- An Adaptive Mapping Method Using Spectral Envelope Approach for DNA Spectral Analysis.Entropy (Basel, Switzerland) · 2022Article
- The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2.Molecular biology and evolution · 2021Article
- periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA.F1000Research · 2021Article
- Article
- Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?RNA biology · 2020Article
- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
- Categorical spectral analysis of periodicity in nucleosomal DNA.Nucleic acids research · 2016Article
Corrections and comments
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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
Periodicity in nucleotide sequences arises from regular repeating patterns which may reflect important structure and function. Although a three-base periodicity in coding regions has been known for some time and has provided the basis for powerful gene prediction algorithms, its origins are still not fully understood. Here, we show that, contrary to common belief, amino acid (AA) bias and codon usage bias are insufficient to create base-3 periodicity. This article applies the rigorous method of spectral envelope to systematically characterize the contributions of codon bias, AA bias and protein structural motifs to the three-base periodicity of coding sequences. The method is also used to classify CpG islands in the human genome. In addition, we show how spectral envelope can be used to trace the evolution of viral genomes and monitor global sequence changes without having to align to previously known genomes. This approach also detects reassortment events, such as those that led to the 2009 pandemic H1N1 virus.
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Registered trials
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