A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes.

ABSTRACT:

Background

Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally intensive. To address this problem, a strategy consisting of sieving (pre-selecting closely related genomes) followed by alignment and calculation has been proposed.

Results

Here, we initially test a published approach called "genome-wide tetranucleotide frequency correlation coefficient" (TETRA), which is specially tailored for sieving. Our results show that sieving by TETRA requires > 40% completeness for both genomes of a pair to yield > 95% sensitivity, indicating that TETRA is completeness-dependent. Accordingly, we develop a novel algorithm called "fragm

SUBMITTER: Zhou Y 

PROVIDER: S-EPMC7045542 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature