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 empi

SUBMITTER: Cong Y 

PROVIDER: S-EPMC4958984 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature