Detecting horizontally transferred and essential genes based on dinucleotide relative abundance.

ABSTRACT: Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i)

SUBMITTER: Baran RH 

PROVIDER: S-EPMC2575891 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature