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Microbe-ID: an open source toolbox for microbial genotyping and species identification. | LitMetric

Microbe-ID: an open source toolbox for microbial genotyping and species identification.

PeerJ

Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.

Published: September 2016

AI Article Synopsis

  • * Microbe-ID includes two main components: Sequence-ID for species identification using sequence queries against a reference database, and Genotype-ID for placing multilocus markers into networks to identify genetic relationships.
  • * The public website, microbe-id.org, offers tools specifically for the genus Phytophthora, allowing users to identify strains and species based on genetic markers, with all code provided openly for accessibility.

Article Abstract

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994078PMC
http://dx.doi.org/10.7717/peerj.2279DOI Listing

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