Phylotyper: in silico predictor of gene subtypes.
Bioinformatics
; 33(22): 3638-3641, 2017 Nov 15.
Article
em En
| MEDLINE
| ID: mdl-29036291
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. AVAILABILITY AND IMPLEMENTATION Phylotyper is a python and R package. It is available from https//github.com/superphy/insilico-subtyping. CONTACT matthew.whiteside@phac-aspc.gc.ca. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Bactérias
/
Infecções Bacterianas
/
Simulação por Computador
/
Surtos de Doenças
/
Sequenciamento Completo do Genoma
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2017
Tipo de documento:
Article
País de afiliação:
Canadá