E. coli functional genotyping: predicting phenotypic traits from whole genome sequences

In this tutorial we will screen genome sequences of Escherichia coli samples for phenotypic traits using the E. coli functional genotyping plugin. This plugin contains public databases for serotype, virulence and resistance prediction, as well as plasmid and prophage detection. An in silico PCR tool is also implemented, making it possible to detect Shiga toxin gene subtypes and virulence genes, mimicking the wet lab PCR.

Sequences

Nucleic acid or amino acid sequences, from import and assembly over multiple alignment to annotation, SNP analysis, primer design and comparison of complete chromosomes.

Download PDF file: 
Download demonstration database: 
WGS demo database for Escherichia coli

Demonstration database containing data for a set of 60 Escherichia coli isolates. This database uses publicly available next-generation sequence reads from the Sequence Read Archive (SRA). For each isolate, NGS reads were de novo assembled into genome sequences. wgMLST alleles were called using the assembly-based and assembly-free method.

Note that the downloaded database backup file (.bnbk) can be restored via the Restore database... functionality in the BioNumerics startup screen.

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