title: A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.
abstract: Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.
authors.affiliation: Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Yingnan
authors.initials: Y
authors.lastname: Cong
authors.affiliation: School of Mathematics and Statistics, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia.
authors.forename: Yao-Ban
authors.initials: YB
authors.lastname: Chan
authors.affiliation: Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ragan
mesh_terms: D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016678:Genome; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*