Barcoding Bacteria

Advances in genotyping assays have resulted in commercially available, costeffective whole-genome analyses. Once relegated to major genomics centers, genotyping capabilities are now spreading to smaller academic and industrial labs worldwide. With vast numbers of microbial sequences published in online databases, there is increasing interest in not only detecting the presence of pathogens, but also determining their relative virulence. Strain differentiation is a prime application for genomic barcoding, whereby microarrays are used to detect a pattern, or signature, based on the presence or absence of multiple genomic sequences. Commercially available software is used to import and align tens of sequences, output as a text file. It is highly time consuming to visually search for informative sections in these alignment files, as they are often thousands to tens of thousands of characters long. Manually developing a phylogenetic tree based on the classification calls of individual SNPs is very inefficient and prone to errors. A computer program designed to choose SNPs from alignment files would greatly simplify the genotyping assay development process.