PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing.
Bioinformatics
; 36(8): 2337-2344, 2020 04 15.
Article
en En
| MEDLINE
| ID: mdl-31899493
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.
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1
Bases de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Genómica
Tipo de estudio:
Diagnostic_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2020
Tipo del documento:
Article
País de afiliación:
Bélgica