ArticleScientific reports2016
Exploring lateral genetic transfer among microbial genomes using TF-IDF.
Article in Scientific reports, 2016. 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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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- Genome language modeling (GLM): a beginner's cheat sheet.Biology methods & protocols · 2025Article
- INSIDER: alignment-free detection of foreign DNA sequences.Computational and structural biotechnology journal · 2021Article
- Alignment-free inference of hierarchical and reticulate phylogenomic relationships.Briefings in bioinformatics · 2019Review
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.Frontiers in microbiology · 2018Article
- Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.Frontiers in microbiology · 2017Article
- A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.Scientific reports · 2016Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
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Abstract
Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.
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