ArticlePloS one2011
Minimal absent words in four human genome assemblies.
Article in PloS one, 2011. 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.
- Zimin patterns in genomes.PLoS computational biology · 2026Article
- Cellular Activity of CQWW Nullomer-Derived Peptides.ACS omega · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution.Genome biology · 2021Article
- Absent words and the (dis)similarity analysis of DNA sequences: an experimental study.BMC research notes · 2016Article
- Linear-time computation of minimal absent words using suffix array.BMC bioinformatics · 2014Article
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Authors and funding
2 authors.
Funding
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Abstract
Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species.
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