期刊
BIOINFORMATICS
卷 36, 期 8, 页码 2337-2344出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz964
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资金
- BCCM/LMG Bacteria Collection
- Belgian Nuclear Research Centre (SCK_CEN)
- Federal Public Planning Service-Science Policy, Belgium
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.
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