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- Title
Phylotyper: in silico predictor of gene subtypes.
- Authors
Whiteside, Matthew D.; Gannon, Victor P. J.; Laing, Chad R.
- Abstract
Summary: Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subtype prediction from gene sequences. Designed for incorporation into WGS pipelines, it is a general prediction tool that can be applied to different subtype schemes. Phylotyper uses phylogeny to model the evolution of the subtype and infer subtypes for unannotated sequences. The phylogenic framework in Phylotyper improves accuracy over approaches based solely on sequence similarity and provides useful contextual feedback.
- Subjects
NUCLEOTIDE sequencing; GENE expression; MEDICAL microbiology; POLYMERASE chain reaction; NUCLEOTIDE sequence
- Publication
Bioinformatics, 2017, Vol 33, Issue 22, p3638
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btx459