ArticleNucleic acids research2021
Significant non-existence of sequences in genomes and proteomes.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Zimin patterns in genomes.PLoS computational biology · 2026Article
- Derivation of oligonucleotide barcodes that are absent from natural sequences.Bioinformatics advances · 2026Article
- Leveraging sequences missing from the human genome to diagnose cancer.Communications medicine · 2025Article
- MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files.BMC bioinformatics · 2025Article
- Article
- Cellular Activity of CQWW Nullomer-Derived Peptides.ACS omega · 2025Article
- Identification of the shortest species-specific oligonucleotide sequences.Genome research · 2025Article
- Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups.bioRxiv : the preprint server for biology · 2025Article
- Investigating DNA words and their distributions across the tree of life.Computational and structural biotechnology journal · 2025Article
- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The fitness cost of spurious phosphorylation.The EMBO journal · 2024Article
- The determinants of the rarity of nucleic and peptide short sequences in nature.NAR genomics and bioinformatics · 2024Article
- Utilizing nullomers in cell-free RNA for early cancer detection.Cancer gene therapy · 2024Article
- Article
- Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.BMC genomics · 2023Article
- The fitness cost of spurious phosphorylation.bioRxiv : the preprint server for biology · 2023Article
- Structural underpinnings of mutation rate variations in the human genome.Nucleic acids research · 2023Article
- Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution.Genome biology · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Minimal absent words (MAWs) are minimal-length oligomers absent from a genome or proteome. Although some artificially synthesized MAWs have deleterious effects, there is still a lack of a strategy for the classification of non-occurring sequences as potentially malicious or benign. In this work, by using Markovian models with multiple-testing correction, we reveal significant absent oligomers, which are statistically expected to exist. This suggests that their absence is due to negative selection. We survey genomes and proteomes covering the diversity of life and find thousands of significant absent sequences. Common significant MAWs are often mono- or dinucleotide tracts, or palindromic. Significant viral MAWs are often restriction sites and may indicate unknown restriction motifs. Surprisingly, significant mammal genome MAWs are often present, but rare, in other mammals, suggesting that they are suppressed but not completely forbidden. Significant human MAWs are frequently present in prokaryotes, suggesting immune function, but rarely present in human viruses, indicating viral mimicry of the host. More than one-fourth of human proteins are one substitution away from containing a significant MAW, with the majority of replacements being predicted harmful. We provide a web-based, interactive database of significant MAWs across genomes and proteomes.
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