ArticleNAR genomics and bioinformatics2024
The determinants of the rarity of nucleic and peptide short sequences in nature.
Article in NAR genomics and bioinformatics, 2024. 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.
- Tracking Down the Evolution of Microorganisms by Exhaustive Bottom-Up Analysis of Proteomes.International journal of molecular sciences · 2025Article
- Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci.Protein science : a publication of the Protein Society · 2025Article
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
- Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups.bioRxiv : the preprint server for biology · 2025Article
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
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Authors and funding
7 authors.
Funding
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Abstract
The prevalence of nucleic and peptide short sequences across organismal genomes and proteomes has not been thoroughly investigated. We examined 45 785 reference genomes and 21 871 reference proteomes, spanning archaea, bacteria, eukaryotes and viruses to calculate the rarity of short sequences in them. To capture this, we developed a metric of the rarity of each sequence in nature, the rarity index. We find that the frequency of certain dipeptides in rare oligopeptide sequences is hundreds of times lower than expected, which is not the case for any dinucleotides. We also generate predictive regression models that infer the rarity of nucleic and proteomic sequences across nature or within each domain of life and viruses separately. When examining each of the three domains of life and viruses separately, the
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Registered trials
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