Genome sequence-based species delimitation with confidence intervals and improved distance functions.

ABSTRACT:

Background

For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an applicati

SUBMITTER: Meier-Kolthoff JP 

PROVIDER: S-EPMC3665452 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature