Ontology highlight
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 and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses.Availability and implementation
The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Goussarov G
PROVIDER: S-EPMC7178395 | biostudies-literature | 2020 Apr
REPOSITORIES: biostudies-literature
Goussarov Gleb G Cleenwerck Ilse I Mysara Mohamed M Leys Natalie N Monsieurs Pieter P Tahon Guillaume G Carlier Aurélien A Vandamme Peter P Van Houdt Rob R
Bioinformatics (Oxford, England) 20200401 8
<h4>Motivation</h4>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-oligonuc ...[more]