ArticleMobile DNA2019
AluMine: alignment-free method for the discovery of polymorphic Alu element insertions.
Article in Mobile DNA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data.Genome biology · 2025Article
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.Scientific reports · 2023Article
- Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.Life (Basel, Switzerland) · 2022Review
- AnNAR genomics and bioinformatics · 2022Article
- The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity.Genome biology and evolution · 2020Article
- TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short
resultsWe have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration.
conclusionsAluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
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