Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.

ABSTRACT: Horizontal gene transfer (HGT) plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and [Formula: see text] that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance. We also studied the influence of different factors such as evoluti

SUBMITTER: Tang K 

PROVIDER: S-EPMC5911508 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature