Extracting subsequences from (whole genome) sequences

In this tutorial we will screen a set of whole genome sequences of some Staphylococcus aureus samples for the presence of the mecA sequence. The assembled sequences present in the whole genome demonstration database of Staphylococcus aureus are used in this tutorial.

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 sample data: 
mecA reference sequence
FASTA sequence of the mecA gene of Staphylococcus aureus for use with the Sequence extraction plugin.
Download demonstration database: 
WGS demo database for Staphylococcus aureus

Demonstration database containing data for a set of 97 Staphylococcus aureus isolates originating from three published studies. 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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