PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing.

ABSTRACT:

Motivation

One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.

Results

Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA

SUBMITTER: Goussarov G 

PROVIDER: S-EPMC7178395 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature